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Current Topics in Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 1568-0266
ISSN (Online): 1873-4294

Review Article

Machine Learning and Artificial Intelligence: A Paradigm Shift in Big Data-Driven Drug Design and Discovery

Author(s): Purvashi Pasrija, Prakash Jha, Pruthvi Upadhyaya, Mohd. Shoaib Khan* and Madhu Chopra*

Volume 22, Issue 20, 2022

Published on: 25 August, 2022

Page: [1692 - 1727] Pages: 36

DOI: 10.2174/1568026622666220701091339

Price: $65

Abstract

Background: The lengthy and expensive process of developing a novel medicine often takes many years and entails a significant financial burden due to its poor success rate. Furthermore, the processing and analysis of quickly expanding massive data necessitate the use of cutting-edge methodologies. As a result, Artificial Intelligence-driven methods that have been shown to improve the efficiency and accuracy of drug discovery have grown in favor.

Objective: The goal of this thorough analysis is to provide an overview of the drug discovery and development timeline, various approaches to drug design, and the use of Artificial Intelligence in many aspects of drug discovery.

Methods: Traditional drug development approaches and their disadvantages have been explored in this paper, followed by an introduction to AI-based technology. Also, advanced methods used in Machine Learning and Deep Learning are examined in detail. A few examples of big data research that has transformed the field of medication discovery have also been presented. Also covered are the many databases, toolkits, and software available for constructing Artificial Intelligence/Machine Learning models, as well as some standard model evaluation parameters. Finally, recent advances and uses of Machine Learning and Deep Learning in drug discovery are thoroughly examined, along with their limitations and future potential.

Conclusion: Artificial Intelligence-based technologies enhance decision-making by utilizing the abundantly available high-quality data, thereby reducing the time and cost involved in the process. We anticipate that this review would be useful to researchers interested in Artificial Intelligencebased drug development.

Keywords: Medicinal chemistry, Quantitative structure-activity relationship, Drug discovery, Computer-aided drug design, Big data, Artificial intelligence, Machine learning, Deep learning.

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[1]
Hughes, J.P.; Rees, S.; Kalindjian, S.B.; Philpott, K.L. Principles of early drug discovery. Br. J. Pharmacol., 2011, 162(6), 1239-1249.
[http://dx.doi.org/10.1111/j.1476-5381.2010.01127.x] [PMID: 21091654]
[2]
DiMasi, J.A.; Grabowski, H.G.; Hansen, R.W. Innovation in the pharmaceutical industry: New estimates of R&D costs. J. Health Econ., 2016, 47, 20-33.
[http://dx.doi.org/10.1016/j.jhealeco.2016.01.012] [PMID: 26928437]
[3]
Gupta, R.; Srivastava, D.; Sahu, M.; Tiwari, S.; Ambasta, R.K.; Kumar, P. Artificial intelligence to deep learning: Machine intelligence approach for drug discovery. Mol. Divers., 2021, 25(3), 1315-1360.
[4]
Kohli, S. Integrated approach to nature as source of new drug lead. In: Molecular Insight of Drug Design; Parikesit, A.A., Ed.; InTech, 2018.
[http://dx.doi.org/10.5772/intechopen.74961]
[5]
Mishra, B.B.; Tiwari, V.K. Natural products: An evolving role in future drug discovery. Eur. J. Med. Chem., 2011, 46(10), 4769-4807.
[http://dx.doi.org/10.1016/j.ejmech.2011.07.057] [PMID: 21889825]
[6]
Tan, S.Y.; Tatsumura, Y. Alexander Fleming. Discoverer of penicillin. Singapore Med. J., 2015, 56(7), 366-367.
[http://dx.doi.org/10.11622/smedj.2015105] [PMID: 26243971]
[7]
Goldstein, I.; Burnett, A.L.; Rosen, R.C.; Park, P.W.; Stecher, V.J. The serendipitous story of sildenafil: An unexpected oral therapy for erectile dysfunction. Sex. Med. Rev., 2019, 7(1), 115-128.
[http://dx.doi.org/10.1016/j.sxmr.2018.06.005] [PMID: 30301707]
[8]
Arabi, A.A. Artificial intelligence in drug design: Algorithms, applications, challenges and ethics. Future Drug Discov., 2021, 3(2), FDD59.
[http://dx.doi.org/10.4155/fdd-2020-0028]
[9]
Pinzi, L.; Rastelli, G. Molecular docking: Shifting paradigms in drug discovery. Int. J. Mol. Sci., 2019, 20(18), 4331.
[http://dx.doi.org/10.3390/ijms20184331] [PMID: 31487867]
[10]
Batool, M.; Ahmad, B.; Choi, S. A structure-based drug discovery paradigm. Int. J. Mol. Sci., 2019, 20(11), 2783.
[http://dx.doi.org/10.3390/ijms20112783] [PMID: 31174387]
[11]
Liu, X.; Shi, D.; Zhou, S.; Liu, H.; Liu, H.; Yao, X. Molecular dynamics simulations and novel drug discovery. Expert Opin. Drug Discov., 2018, 13(1), 23-37.
[http://dx.doi.org/10.1080/17460441.2018.1403419] [PMID: 29139324]
[12]
Li, J.W.H.; Vederas, J.C. Drug discovery and natural products: End of an era or an endless frontier? Science, 2009, 325(5937), 161-165.
[http://dx.doi.org/10.1126/science.1168243] [PMID: 19589993]
[13]
Saikia, S.; Bordoloi, M. Molecular docking: Challenges, advances and its use in drug discovery perspective. Curr. Drug Targets, 2019, 20(5), 501-521.
[http://dx.doi.org/10.2174/1389450119666181022153016] [PMID: 30360733]
[14]
Lambrinidis, G.; Tsantili-Kakoulidou, A. Challenges with multi-objective QSAR in drug discovery. Expert Opin. Drug Discov., 2018, 13(9), 851-859.
[http://dx.doi.org/10.1080/17460441.2018.1496079] [PMID: 29996683]
[15]
Pearlstein, R.A.; Wan, H.; Aravamuthan, V. Toward in vivo relevant drug design. Drug Discov. Today, 2021, 26(3), 637-650.
[http://dx.doi.org/10.1016/j.drudis.2020.10.012] [PMID: 33132106]
[16]
Emwas, A.H.; Szczepski, K.; Poulson, B.G.; Chandra, K.; McKay, R.T.; Dhahri, M.; Alahmari, F.; Jaremko, L.; Lachowicz, J.I.; Jaremko, M. NMR as a “Gold Standard” method in drug design and discovery. Molecules, 2020, 25(20), 4597.
[http://dx.doi.org/10.3390/molecules25204597] [PMID: 33050240]
[17]
van Montfort, R.L.M.; Workman, P. Structure-based drug design: Aiming for a perfect fit. Essays Biochem., 2017, 61(5), 431-437.
[http://dx.doi.org/10.1042/EBC20170052] [PMID: 29118091]
[18]
Jenkinson, S.; Schmidt, F.; Rosenbrier Ribeiro, L.; Delaunois, A.; Valentin, J.P. A practical guide to secondary pharmacology in drug discovery. J. Pharmacol. Toxicol. Methods, 2020, 105, 106869.
[http://dx.doi.org/10.1016/j.vascn.2020.106869] [PMID: 32302774]
[19]
Henninot, A.; Collins, J.C.; Nuss, J.M. The current state of peptide drug discovery: Back to the future? J. Med. Chem., 2018, 61(4), 1382-1414.
[http://dx.doi.org/10.1021/acs.jmedchem.7b00318] [PMID: 28737935]
[20]
Kirsch, P.; Hartman, A.M.; Hirsch, A.K.H.; Empting, M. Concepts and core principles of fragment-based drug design. Molecules, 2019, 24(23), 4309.
[http://dx.doi.org/10.3390/molecules24234309] [PMID: 31779114]
[21]
Mandal, S.; Moudgil, M.; Mandal, S.K. Rational drug design. Eur. J. Pharmacol., 2009, 625(1-3), 90-100.
[http://dx.doi.org/10.1016/j.ejphar.2009.06.065] [PMID: 19835861]
[22]
Swinney, D.C.; Anthony, J. How were new medicines discovered? Nat. Rev. Drug Discov., 2011, 10(7), 507-519.
[http://dx.doi.org/10.1038/nrd3480] [PMID: 21701501]
[23]
Padmanabhan, S.; Ravella, S.; Curiel, T.; Giles, F. Current status of therapy for chronic myeloid leukemia: A review of drug development. Future Oncol., 2008, 4(3), 359-377.
[http://dx.doi.org/10.2217/14796694.4.3.359] [PMID: 18518762]
[24]
Pârvu, L. QSAR - a piece of drug design. J. Cell. Mol. Med., 2003, 7(3), 333-335.
[http://dx.doi.org/10.1111/j.1582-4934.2003.tb00235.x] [PMID: 14594559]
[25]
Meng, X.Y.; Zhang, H.X.; Mezei, M.; Cui, M. Molecular docking: A powerful approach for structure-based drug discovery. Curr. Comput.-. Aid. Drug Des., 2011, 7(2), 146-157.
[http://dx.doi.org/10.2174/157340911795677602] [PMID: 21534921]
[26]
Talele, T.; Khedkar, S.; Rigby, A. Successful applications of computer aided drug discovery: Moving drugs from concept to the clinic. Curr. Top. Med. Chem., 2010, 10(1), 127-141.
[http://dx.doi.org/10.2174/156802610790232251] [PMID: 19929824]
[27]
Lounnas, V.; Ritschel, T.; Kelder, J.; McGuire, R.; Bywater, R.P.; Foloppe, N. Current progress in structure-based rational drug design marks a new mindset in drug discovery. Comput. Struct. Biotechnol. J., 2013, 5(6), e201302011.
[http://dx.doi.org/10.5936/csbj.201302011] [PMID: 24688704]
[28]
Marshall, G.R. Limiting assumptions in structure-based design: Binding entropy. J. Comput. Aided Mol. Des., 2012, 26(1), 3-8.
[http://dx.doi.org/10.1007/s10822-011-9494-1] [PMID: 22212342]
[29]
Naderi, M.; Alvin, C.; Ding, Y.; Mukhopadhyay, S.; Brylinski, M. A graph-based approach to construct target-focused libraries for virtual screening. J. Cheminform., 2016, 8(1), 14.
[http://dx.doi.org/10.1186/s13321-016-0126-6] [PMID: 26981157]
[30]
Drews, J. Drug discovery: A historical perspective. Science, 2000, 287(5460), 1960-1964.
[31]
Sliwoski, G.; Kothiwale, S.; Meiler, J.; Lowe, E.W., Jr. Computational methods in drug discovery. Pharmacol. Rev., 2014, 66(1), 334-395.
[http://dx.doi.org/10.1124/pr.112.007336] [PMID: 24381236]
[32]
Bielska, E.; Lucas, X.; Czerwoniec, A.; Kasprzak, J.M.; Kaminska, K.H.; Bujnicki, J.M. Virtual screening strategies in drug design – Methods and applications. BioTechnologia, 2014, 92, 249-264.
[33]
Stoddart, L.A.; White, C.W.; Nguyen, K.; Hill, S.J.; Pfleger, K.D.G. Fluorescence- and bioluminescence-based approaches to study GPCR ligand binding. Br. J. Pharmacol., 2016, 173(20), 3028-3037.
[http://dx.doi.org/10.1111/bph.13316] [PMID: 26317175]
[34]
Fox, S.; Farr-Jones, S.; Sopchak, L.; Boggs, A.; Nicely, H.W.; Khoury, R.; Biros, M. High-throughput screening: Update on practices and success. SLAS Discov., 2006, 11(7), 864-869.
[http://dx.doi.org/10.1177/1087057106292473] [PMID: 16973922]
[35]
Bleicher, K.H.; Böhm, H.J.; Müller, K.; Alanine, A.I. Hit and lead generation: Beyond high-throughput screening. Nat. Rev. Drug Discov., 2003, 2(5), 369-378.
[http://dx.doi.org/10.1038/nrd1086] [PMID: 12750740]
[36]
Yang, Z.Y.; He, J.H.; Lu, A.P.; Hou, T.J.; Cao, D.S. Frequent hitters: Nuisance artifacts in high-throughput screening. Drug Discov. Today, 2020, 25(4), 657-667.
[http://dx.doi.org/10.1016/j.drudis.2020.01.014] [PMID: 31987936]
[37]
Guan, L.; Yang, H.; Cai, Y.; Sun, L.; Di, P.; Li, W.; Liu, G.; Tang, Y. ADMET-score – a comprehensive scoring function for evaluation of chemical drug-likeness. MedChemComm, 2019, 10(1), 148-157.
[http://dx.doi.org/10.1039/C8MD00472B] [PMID: 30774861]
[38]
Benet, L.Z.; Hosey, C.M.; Ursu, O.; Oprea, T.I. BDDCS, the Rule of 5 and drugability. Adv. Drug Deliv. Rev., 2016, 101, 89-98.
[http://dx.doi.org/10.1016/j.addr.2016.05.007] [PMID: 27182629]
[39]
Mignani, S.; Rodrigues, J.; Tomas, H.; Jalal, R.; Singh, P.P.; Majoral, J.P.; Vishwakarma, R.A. Present drug-likeness filters in medicinal chemistry during the hit and lead optimization process: How far can they be simplified? Drug Discov. Today, 2018, 23(3), 605-615.
[http://dx.doi.org/10.1016/j.drudis.2018.01.010] [PMID: 29330127]
[40]
Cruciani, G.; Carosati, E.; De Boeck, B.; Ethirajulu, K.; Mackie, C.; Howe, T.; Vianello, R. MetaSite: Understanding metabolism in human cytochromes from the perspective of the chemist. J. Med. Chem., 2005, 48(22), 6970-6979.
[http://dx.doi.org/10.1021/jm050529c] [PMID: 16250655]
[41]
Ioakimidis, L.; Thoukydidis, L.; Mirza, A.; Naeem, S.; Reynisson, J. Benchmarking the reliability of QikProp. correlation between experimental and predicted values. QSAR Comb. Sci., 2008, 27(4), 445-456.
[http://dx.doi.org/10.1002/qsar.200730051]
[42]
Ekins, S.; Andreyev, S.; Ryabov, A.; Kirillov, E.; Rakhmatulin, E.A.; Bugrim, A.; Nikolskaya, T. Computational prediction of human drug metabolism. Expert Opin. Drug Metab. Toxicol., 2005, 1(2), 303-324.
[http://dx.doi.org/10.1517/17425255.1.2.303] [PMID: 16922645]
[43]
Optibrium. Stardrop. Available from: https://www.optibrium.com/stardrop/ (Accessed on: Feb 8, 2022).
[44]
BIOVIA. QSAR, ADMET and Predictive Toxicology - BIOVIA - Dassault Systèmes®. Available from: https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/qsar-admet-and-predictive-toxicology/ (Accessed on: Feb 8, 2022).
[45]
Greene, N.; Judson, P.N.; Langowski, J.J.; Marchant, C.A. Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR. SAR QSAR Environ. Res., 1999, 10(2-3), 299-314.
[http://dx.doi.org/10.1080/10629369908039182] [PMID: 10491855]
[46]
Daina, A.; Michielin, O.; Zoete, V. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 2017, 7(1), 42717.
[http://dx.doi.org/10.1038/srep42717] [PMID: 28256516]
[47]
Dhanda, S.K.; Singla, D.; Mondal, A.K.; Raghava, P.S. DrugMint: A webserver for predicting and designing of drug-like molecules. Biol. Direct, 2013, 8, 28.
[48]
Dong, J.; Wang, N.N.; Yao, Z.J.; Zhang, L.; Cheng, Y.; Ouyang, D.; Lu, A.P.; Cao, D.S. ADMETlab: A platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. J. Cheminform., 2018, 10(1), 29.
[http://dx.doi.org/10.1186/s13321-018-0283-x] [PMID: 29943074]
[49]
Sousa, S.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J. Virtual screening in drug design and development. Comb. Chem. High Throughput Screen., 2010, 13(5), 442-453.
[http://dx.doi.org/10.2174/138620710791293001] [PMID: 20236061]
[50]
Tanrikulu, Y.; Krüger, B.; Proschak, E. The holistic integration of virtual screening in drug discovery. Drug Discov. Today, 2013, 18(7-8), 358-364.
[http://dx.doi.org/10.1016/j.drudis.2013.01.007] [PMID: 23340112]
[51]
Oprea, T. Virtual screening in lead discovery: A viewpoint. Molecules, 2002, 7(1), 51-62.
[http://dx.doi.org/10.3390/70100051]
[52]
Szymański, P.; Markowicz, M.; Mikiciuk-Olasik, E. Adaptation of high-throughput screening in drug discovery-toxicological screening tests. Int. J. Mol. Sci., 2011, 13(1), 427-452.
[http://dx.doi.org/10.3390/ijms13010427] [PMID: 22312262]
[53]
Tan, L.; Geppert, H.; Sisay, M.T.; Gütschow, M.; Bajorath, J. Integrating structure‐ and ligand‐based virtual screening: Comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets. ChemMedChem, 2008, 3(10), 1566-1571.
[54]
Lionta, E.; Spyrou, G.; Vassilatis, D.K.; Cournia, Z. Structure-based virtual screening for drug discovery: Principles, applications and recent advances. Curr. Top. Med. Chem., 2014, 14(16), 1923-38.
[55]
Langdon, S.R.; Westwood, I.M.; van Montfort, R.L.M.; Brown, N.; Blagg, J. Scaffold-focused virtual screening: Prospective application to the discovery of TTK inhibitors. J. Chem. Inform. Model., 2013, 53(5), 1100-1112.
[56]
Korb, O.; Olsson, T.S.G.; Bowden, S.J.; Hall, R.J.; Verdonk, M.L.; Liebeschuetz, J.W.; Cole, J.C. Potential and limitations of ensemble docking. J. Chem. Inf. Model., 2012, 52(5), 1262-1274.
[http://dx.doi.org/10.1021/ci2005934] [PMID: 22482774]
[57]
Mendez, D.; Gaulton, A.; Bento, A.P.; Chambers, J.; De Veij, M.; Félix, E.; Magariños, M.P.; Mosquera, J.F.; Mutowo, P.; Nowotka, M.; Gordillo-Marañón, M.; Hunter, F.; Junco, L.; Mugumbate, G.; Rodriguez-Lopez, M.; Atkinson, F.; Bosc, N.; Radoux, C.J.; Segura-Cabrera, A.; Hersey, A.; Leach, A.R. ChEMBL: Towards direct deposition of bioassay data. Nucleic Acids Res., 2019, 47(D1), D930-D940.
[http://dx.doi.org/10.1093/nar/gky1075] [PMID: 30398643]
[58]
Kim, S.; Chen, J.; Cheng, T.; Gindulyte, A.; He, J.; He, S.; Li, Q.; Shoemaker, B.A.; Thiessen, P.A.; Yu, B.; Zaslavsky, L.; Zhang, J.; Bolton, E.E. PubChem 2019 update: Improved access to chemical data. Nucleic Acids Res., 2019, 47(D1), D1102-D1109.
[59]
Thermofisher Scientific. Maybridge. Available from: https://www. thermofisher.in/chemicals/en/brands/maybridge.html (Accessed on: Feb 15, 2022).
[60]
Wishart, D.S.; Feunang, Y.D.; Guo, A.C.; Lo, E.J.; Marcu, A.; Grant, J.R.; Sajed, T.; Johnson, D.; Li, C.; Sayeeda, Z.; Assempour, N.; Iynkkaran, I.; Liu, Y.; Maciejewski, A.; Gale, N.; Wilson, A.; Chin, L.; Cummings, R.; Le, D.; Pon, A.; Knox, C.; Wilson, M. DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Res., 2018, 46(D1), D1074-D1082.
[http://dx.doi.org/10.1093/nar/gkx1037] [PMID: 29126136]
[61]
NCI/CADD Group. Chemoinformatics tools and user services., Available from: https://cactus.nci.nih.gov/ (Accessed on: Feb 15, 2022).
[62]
Sethi, A.; Joshi, K.; Sasikala, K.; Alvala, M. Molecular docking in modern drug discovery: Principles and recent applications. IntechOpen, Available from: https://www.intechopen.com/chapters/67939 (Accessed on Feb 8, 2022).
[63]
Sandor, V.; Kozakov, D. Sampling and scoring: A marriage made in heaven - Vajda - 2013 - Proteins: Structure, function, and bioinformatics. Proteins, 2013, 81(11), 1874-1884.
[64]
Ross, G.A.; Morris, G.M.; Biggin, P.C. One size does not fit all: The limits of structure-based models in drug discovery. J. Chem. Theory Comput., 2013, 9(9), 4266-4274.
[65]
Guedes, I.A.; Pereira, F.S.S.; Dardenne, L.E. Empirical Scoring Functions for Structure-Based virtual screening: Applications, critical aspects, and challenges. Front. Pharmacol., 2018, 9, 1089.
[http://dx.doi.org/10.3389/fphar.2018.01089] [PMID: 30319422]
[66]
Truchon, J.F.; Bayly, C.I. Evaluating virtual screening methods: Good and bad metrics for the “early recognition” problem. J. Chem. Inf. Model., 2007, 47(2), 488-508.
[http://dx.doi.org/10.1021/ci600426e] [PMID: 17288412]
[67]
Maia, E.H.B.; Assis, L.C.; de Oliveira, T.A.; da Silva, A.M.; Taranto, A.G. Structure-based virtual screening: From classical to artificial intelligence. Front Chem., 2020, 8, 343.
[http://dx.doi.org/10.3389/fchem.2020.00343] [PMID: 32411671]
[68]
Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 2010, 31(2), 455-461.
[PMID: 19499576]
[69]
Wu, G.; Robertson, D.H.; Brooks, C.L., III; Vieth, M. Detailed analysis of grid-based molecular docking: A case study of cdocker?a charmm-based MD docking algorithm. J. Comput. Chem., 2003, 24(13), 1549-1562.
[http://dx.doi.org/10.1002/jcc.10306] [PMID: 12925999]
[70]
Kozakov, D.; Hall, D.R.; Xia, B.; Porter, K.A.; Padhorny, D.; Yueh, C.; Beglov, D.; Vajda, S. The ClusPro web server for protein–protein docking. Nat. Protoc., 2017, 12(2), 255-278.
[http://dx.doi.org/10.1038/nprot.2016.169] [PMID: 28079879]
[71]
Stroganov, O.V.; Novikov, F.N.; Stroylov, V.S.; Kulkov, V.; Chilov, G.G. Lead finder: An approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening. J. Chem. Inf. Model., 2008, 48(12), 2371-2385.
[http://dx.doi.org/10.1021/ci800166p] [PMID: 19007114]
[72]
Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins, 1999, 37(2), 228-241.
[http://dx.doi.org/10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8] [PMID: 10584068]
[73]
Verdonk, M.L.; Cole, J.C.; Hartshorn, M.J.; Murray, C.W.; Taylor, R.D. Improved protein-ligand docking using GOLD. Proteins, 2003, 52(4), 609-623.
[http://dx.doi.org/10.1002/prot.10465] [PMID: 12910460]
[74]
Rao, S.N.; Head, M.S.; Kulkarni, A.; LaLonde, J.M. Validation studies of the site-directed docking program LibDock. J. Chem. Inf. Model., 2007, 47(6), 2159-2171.
[http://dx.doi.org/10.1021/ci6004299] [PMID: 17985863]
[75]
Venkatachalam, C.M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model., 2003, 21(4), 289-307.
[http://dx.doi.org/10.1016/S1093-3263(02)00164-X] [PMID: 12479928]
[76]
Pierce, B.G.; Wiehe, K.; Hwang, H.; Kim, B.H.; Vreven, T.; Weng, Z. ZDOCK server: Interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics, 2014, 30(12), 1771-1773.
[http://dx.doi.org/10.1093/bioinformatics/btu097] [PMID: 24532726]
[77]
Dixon, S.L.; Smondyrev, A.M.; Rao, S.N. PHASE: A novel approach to pharmacophore modeling and 3D database searching. Chem. Biol. Drug Des., 2006, 67(5), 370-372.
[http://dx.doi.org/10.1111/j.1747-0285.2006.00384.x] [PMID: 16784462]
[78]
Kaserer, T.; Beck, K.R.; Akram, M.; Odermatt, A.; Schuster, D. Pharmacophore models and pharmacophore-based virtual screening: Concepts and applications exemplified on hydroxysteroid dehydrogenases. Molecules, 2015, 20(12), 22799-832.
[79]
Ferreira, L.G.; Dos Santos, R.N.; Oliva, G.; Andricopulo, A.D. Molecular docking and structure-based drug design strategies. Molecules, 2015, 20(7), 13384-13421.
[80]
Akhtar, N.; Jabeen, I.; Jalal, N.; Antilla, J. Structure-based pharmacophore models to probe anticancer activity of inhibitors of protein kinase B-beta (PKB β). Chem. Biol. Drug Des., 2019, 93(3), 325-336.
[81]
Li, Q. Application of fragment-based drug discovery to versatile targets. Front. Mol. Biosci., 2020, 7, 180.
[http://dx.doi.org/10.3389/fmolb.2020.00180] [PMID: 32850968]
[82]
de Souza Neto, L.R.; Moreira-Filho, J.T.; Neves, B.J.; Maidana, R.L.B.; Guimarães, A.C.R.; Furnham, N.; Andrade, C.H.; Silva, Jr. F.P. In silico strategies to support fragment-to-lead optimization in drug discovery. Front Chem., 2020, 8, 93.
[83]
Jhoti, H.; Williams, G.; Rees, D.C.; Murray, C.W. The “rule of three” for fragment-based drug discovery: Where are we now? Nat. Rev. Drug Discov., 2013, 12(8), 644-645.
[84]
Keeley, A.; Petri, L.; Ábrányi-Balogh, P.; Keserű, G.M. Covalent fragment libraries in drug discovery. Drug Discov. Today, 2020, 25(6), 983-996.
[http://dx.doi.org/10.1016/j.drudis.2020.03.016] [PMID: 32298798]
[85]
Nicholls, A.; McGaughey, G.B.; Sheridan, R.P.; Good, A.C.; Warren, G.; Mathieu, M.; Muchmore, S.W.; Brown, S.P.; Grant, J.A.; Haigh, J.A.; Nevins, N.; Jain, A.N.; Kelley, B. Molecular shape and medicinal chemistry: A perspective. J. Med. Chem., 2010, 53(10), 3862-3886.
[http://dx.doi.org/10.1021/jm900818s] [PMID: 20158188]
[86]
Fan, F.; Warshaviak, D.T.; Hamadeh, H.K.; Dunn, R.T. The integration of pharmacophore-based 3D QSAR modeling and virtual screening in safety profiling: A case study to identify antagonistic activities against adenosine receptor, A2A, using 1,897 known drugs. PLoS One, 2019, 14(1), e0204378.
[87]
Kunimoto, R.; Bajorath, J. Combining similarity searching and network analysis for the identification of active compounds. ACS Omega, 2018, 3(4), 3768-3777.
[http://dx.doi.org/10.1021/acsomega.8b00344] [PMID: 30023879]
[88]
Cumming, J.G.; Davis, A.M.; Muresan, S.; Haeberlein, M.; Chen, H. Chemical predictive modelling to improve compound quality. Nat. Rev. Drug Discov., 2013, 12(12), 948-962.
[89]
Pal, S.; Kumar, V.; Kundu, B.; Bhattacharya, D.; Preethy, N.; Reddy, M.P.; Talukdar, A. Ligand-based pharmacophore modeling, virtual screening and molecular docking studies for discovery of potential Topoisomerase I Inhibitors. Comput. Struct. Biotechnol. J., 2019, 17, 291-310.
[http://dx.doi.org/10.1016/j.csbj.2019.02.006] [PMID: 30867893]
[90]
Verma, P.; Dalal, K.; Chopra, M. Pharmacophore development and screening for discovery of potential inhibitors of ADAMTS-4 for osteoarthritis therapy. J. Mol. Model., 2016, 22(8), 178.
[http://dx.doi.org/10.1007/s00894-016-3035-8] [PMID: 27401455]
[91]
Li, S.; Zhang, S.; Chen, D.; Jiang, X.; Liu, B.; Zhang, H.; Rachakunta, M.; Zuo, Z. Identification of novel TRPC5 inhibitors by pharmacophore-based and structure-based approaches. Comput. Biol. Chem., 2020, 87, 107302.
[http://dx.doi.org/10.1016/j.compbiolchem.2020.107302] [PMID: 32554176]
[92]
Noha, S.M.; Jazzar, B.; Kuehnl, S.; Rollinger, J.M.; Stuppner, H.; Schaible, A.M.; Werz, O.; Wolber, G.; Schuster, D. Pharmacophore-based discovery of a novel cytosolic phospholipase A2α inhibitor. Bioorg. Med. Chem. Lett., 2012, 22(2), 1202-1207.
[http://dx.doi.org/10.1016/j.bmcl.2011.11.093] [PMID: 22192589]
[93]
Greenidge, P.A.; Carlsson, B.; Bladh, L.G.; Gillner, M. Pharmacophores incorporating numerous excluded volumes defined by X-ray crystallographic structure in three-dimensional database searching: Application to the thyroid hormone receptor. J. Med. Chem., 1998, 41(14), 2503-2512.
[http://dx.doi.org/10.1021/jm9708691] [PMID: 9651155]
[94]
Chopra, M.; Mishra, A.K. Ligand-based molecular modeling study on a chemically diverse series of cholecystokinin-B/gastrin receptor antagonists: Generation of predictive model. J. Chem. Inf. Model., 2005, 45(6), 1934-1942.
[http://dx.doi.org/10.1021/ci050257m] [PMID: 16309300]
[95]
Kumari, S.; Chowdhury, J.; Sikka, M.; Verma, P.; Jha, P.; Mishra, A.K.; Saluja, D.; Chopra, M. Identification of potent cholecystokinin-B receptor antagonists: Synthesis, molecular modeling and anti-cancer activity against pancreatic cancer cells. MedChemComm, 2017, 8(7), 1561-1574.
[http://dx.doi.org/10.1039/C7MD00171A] [PMID: 30108868]
[96]
Chopra, M.; Gupta, R.; Gupta, S.; Saluja, D. Molecular modeling study on chemically diverse series of cyclooxygenase-2 selective inhibitors: Generation of predictive pharmacophore model using Catalyst. J. Mol. Model., 2008, 14(11), 1087-1099.
[http://dx.doi.org/10.1007/s00894-008-0350-8] [PMID: 18665400]
[97]
Hansch, C.; Fujita, T. p-σ-π Analysis. A method for the correlation of biological activity and chemical structure. J. Am. Chem. Soc., 1964, 86(8), 1616-1626.
[98]
Cruciani, G.; Carosati, E.; Clementi, S. 25 - Three-Dimensional Quantitative Structure-Property Relationships. In: The Practice of Medicinal Chemistry, 2nd ed; Wermuth, C.G., Ed.; Academic Press: London, 2003; pp. 405-416.
[http://dx.doi.org/10.1016/B978-012744481-9/50029-5]
[99]
Sharma, M.; Jha, P.; Verma, P.; Chopra, M. Combined comparative molecular field analysis, comparative molecular similarity indices analysis, molecular docking and molecular dynamics studies of histone deacetylase 6 inhibitors. Chem. Biol. Drug Des., 2019, 93(5), 910-925.
[100]
Sharma, R.; Dhingra, N.; Patil, S. CoMFA, CoMSIA, HQSAR and molecular docking analysis of ionone-based chalcone derivatives as antiprostate cancer activity. Indian J. Pharm. Sci., 2016, 78(1), 54-64.
[101]
Cassano, A.; Manganaro, A.; Martin, T.; Young, D.; Piclin, N.; Pintore, M.; Bigoni, D.; Benfenati, E. CAESAR models for developmental toxicity. Chem. Cent. J., 2010, 29(4)(Suppl. 1), S4.
[102]
Knott, P.J.; Hutson, P.H.; Curzon, G. Fatty acid and tryptophan changes on disturbing groups of rats and caging them singly. Pharmacol. Biochem. Behav., 1977, 7(3), 245-252.
[http://dx.doi.org/10.1016/0091-3057(77)90141-1] [PMID: 563080]
[103]
Potemkin, V.; Grishina, M. Principles for 3D/4D QSAR classification of drugs. Drug Discov. Today, 2008, 13(21-22), 952-959.
[http://dx.doi.org/10.1016/j.drudis.2008.07.006] [PMID: 18721896]
[104]
Mascarenhas, A.M.S.; de Almeida, R.B.M.; de Araujo Neto, M.F.; Mendes, G.O.; da Cruz, J.N.; Dos Santos, C.B.R.; Botura, M.B.; Leite, F.H.A. Pharmacophore-based virtual screening and molecular docking to identify promising dual inhibitors of human acetylcholinesterase and butyrylcholinesterase. J. Biomol. Struct. Dyn., 2021, 39(16), 6021-6030.
[105]
Vukovic, K.; Gadaleta, D.; Benfenati, E. Methodology of ai-QSAR: A group-specific approach to QSAR modelling. J. Cheminform., 2019, 11, 27.
[106]
Vainio, M.J.; Johnson, M.S. McQSAR: A multiconformational quantitative structure-activity relationship engine driven by genetic algorithms. J. Chem. Inf. Model., 2005, 45(6), 1953-1961.
[http://dx.doi.org/10.1021/ci0501847] [PMID: 16309302]
[107]
Tosco, P.; Balle, T. Open3DQSAR: A new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields. J. Mol. Model., 2011, 17(1), 201-208.
[http://dx.doi.org/10.1007/s00894-010-0684-x] [PMID: 20383726]
[108]
Rácz, A.; Bajusz, D.; Héberger, K. Modelling methods and cross-validation variants in QSAR: A multi-level analysis. SAR QSAR Environ. Res., 2018, 29(9), 661-674.
[109]
Levitt, M. Molecular Dynamics of Hydrogen Bonds in Bovine Pancreatic Trypsin Inhibitor Protein. Nature, 1981, 294(5839), 379-380.
[110]
Jorgensen, W.L. Foundations of biomolecular modeling. Cell, 2013, 155(6), 1199-1202.
[http://dx.doi.org/10.1016/j.cell.2013.11.023] [PMID: 24315087]
[111]
Bunker, A.; Róg, T. Mechanistic Understanding from molecular dynamics simulation in pharmaceutical research 1: Drug delivery. Front. Mol. Biosci., 2020, 7, 604770.
[112]
Hofer, T.S.; de Visser, S.P. Editorial: Quantum mechanical/molecular mechanical approaches for the investigation of chemical systems - recent developments and advanced applications. Front Chem., 2018, 6, 357.
[113]
Case, D.A.; Cheatham, T.E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, Jr. K.M.; Onufriev, A.; Simmerling, C.; Wang, R.; Woods, R.J. The Amber biomolecular simulation programs. J. Comput. Chem., 2005, 26(16), 1668-1688.
[114]
Ivanova, L.; Tammiku-Taul, J.; García-Sosa, A.T.; Sidorova, Y.; Saarma, M.; Karelson, M. Molecular dynamics simulations of the interactions between glial cell line-derived neurotrophic factor family receptor gfrα1 and small-molecule ligands. ACS Omega, 2018, 3(9), 11407-11414.
[115]
Abraham, M.J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J.C.; Hess, B.; Lindahl, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 2015, 1-2, 19-25.
[http://dx.doi.org/10.1016/j.softx.2015.06.001]
[116]
van Aalten, D.M.F.; Bywater, R.; Findlay, J.B.C.; Hendlich, M.; Hooft, R.W.W.; Vriend, G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des., 1996, 10(3), 255-262.
[http://dx.doi.org/10.1007/BF00355047] [PMID: 8808741]
[117]
Lee, J.; Cheng, X.; Swails, J.M.; Yeom, M.S.; Eastman, P.K.; Lemkul, J.A.; Wei, S.; Buckner, J.; Jeong, J.C.; Qi, Y.; Jo, S.; Pande, V.S.; Case, D.A.; Brooks, C.L., III; MacKerell, A.D., Jr; Klauda, J.B. Im, W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J. Chem. Theory Comput., 2016, 12(1), 405-413.
[http://dx.doi.org/10.1021/acs.jctc.5b00935] [PMID: 26631602]
[118]
Abdel-Azeim, S. Revisiting OPLS-AA force field for the simulation of anionic surfactants in concentrated electrolyte solutions. J. Chem. Theory Comput., 2020, 16(2), 1136-1145.
[http://dx.doi.org/10.1021/acs.jctc.9b00947] [PMID: 31904948]
[119]
Christen, M.; Hünenberger, P.H.; Bakowies, D.; Baron, R.; Bürgi, R.; Geerke, D.P.; Heinz, T.N.; Kastenholz, M.A.; Kräutler, V.; Oostenbrink, C.; Peter, C.; Trzesniak, D.; van Gunsteren, W.F. The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem., 2005, 26(16), 1719-1751.
[http://dx.doi.org/10.1002/jcc.20303] [PMID: 16211540]
[120]
Al-Karmalawy, A.A.; Dahab, M.A.; Metwaly, A.M.; Elhady, S.S.; Elkaeed, E.B.; Eissa, I.H.; Darwish, K.M. Molecular docking and dynamics simulation revealed the potential inhibitory activity of ACEIs against SARS-CoV-2 Targeting the hACE2 Receptor. Front Chem., 2021, 9, 661230.
[http://dx.doi.org/10.3389/fchem.2021.661230] [PMID: 34017819]
[121]
Genheden, S.; Ryde, U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin. Drug Discov., 2015, 10(5), 449-461.
[http://dx.doi.org/10.1517/17460441.2015.1032936] [PMID: 25835573]
[122]
Kumari, R.; Kumar, R.; Lynn, A. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model., 2014, 54(7), 1951-1962.
[http://dx.doi.org/10.1021/ci500020m] [PMID: 24850022]
[123]
Vázquez, J.; López, M.; Gibert, E.; Herrero, E.; Luque, F.J. Merging ligand-based and structure-based methods in drug discovery: An overview of combined virtual screening approaches. Molecules, 2020, 25(20), 4723.
[http://dx.doi.org/10.3390/molecules25204723] [PMID: 33076254]
[124]
Atanasov, A.G.; Zotchev, S.B.; Dirsch, V.M.; Supuran, C.T. Natural products in drug discovery: Advances and opportunities. Nat. Rev. Drug Discov., 2021, 20(3), 200-216.
[http://dx.doi.org/10.1038/s41573-020-00114-z] [PMID: 33510482]
[125]
Ondetti, M.A.; Rubin, B.; Cushman, D.W. Design of specific inhibitors of angiotensin-converting enzyme: New class of orally active antihypertensive agents. Science, 1977, 196(4288), 441-444.
[http://dx.doi.org/10.1126/science.191908] [PMID: 191908]
[126]
Buchdunger, E.; Zimmermann, J.; Mett, H.; Meyer, T.; Müller, M.; Druker, B.J.; Lydon, N.B. Inhibition of the Abl protein-tyrosine kinase in vitro and in vivo by a 2-phenylaminopyrimidine derivative. Cancer Res., 1996, 56(1), 100-104.
[PMID: 8548747]
[127]
Li, W.; Escarpe, P.A.; Eisenberg, E.J.; Cundy, K.C.; Sweet, C.; Jakeman, K.J.; Merson, J.; Lew, W.; Williams, M.; Zhang, L.; Kim, C.U.; Bischofberger, N.; Chen, M.S.; Mendel, D.B. Identification of GS 4104 as an orally bioavailable prodrug of the influenza virus neuraminidase inhibitor GS 4071. Antimicrob. Agents Chemother., 1998, 42(3), 647-653.
[http://dx.doi.org/10.1128/AAC.42.3.647] [PMID: 9517946]
[128]
Kempf, D.J.; Marsh, K.C.; Denissen, J.F.; McDonald, E.; Vasavanonda, S.; Flentge, C.A.; Green, B.E.; Fino, L.; Park, C.H.; Kong, X.P. ABT-538 is a potent inhibitor of human immunodeficiency virus protease and has high oral bioavailability in humans. Proc. Natl. Acad. Sci. USA, 1995, 92(7), 2484-2488.
[http://dx.doi.org/10.1073/pnas.92.7.2484] [PMID: 7708670]
[129]
Sham, H.L.; Kempf, D.J.; Molla, A.; Marsh, K.C.; Kumar, G.N.; Chen, C.M.; Kati, W.; Stewart, K.; Lal, R.; Hsu, A.; Betebenner, D.; Korneyeva, M.; Vasavanonda, S.; McDonald, E.; Saldivar, A.; Wideburg, N.; Chen, X.; Niu, P.; Park, C.; Jayanti, V.; Grabowski, B.; Granneman, G.R.; Sun, E.; Japour, A.J.; Leonard, J.M.; Plattner, J.J.; Norbeck, D.W. ABT-378, a highly potent inhibitor of the human immunodeficiency virus protease. Antimicrob. Agents Chemother., 1998, 42(12), 3218-3224.
[http://dx.doi.org/10.1128/AAC.42.12.3218] [PMID: 9835517]
[130]
Falcoz, C.; Jenkins, J.M.; Bye, C.; Hardman, T.C.; Kenney, K.B.; Studenberg, S.; Fuder, H.; Prince, W.T. Pharmacokinetics of GW433908, a prodrug of amprenavir, in healthy male volunteers. J. Clin. Pharmacol., 2002, 42(8), 887-898.
[http://dx.doi.org/10.1177/009127002401102803] [PMID: 12162471]
[131]
Xia, W.; Liu, L.H.; Ho, P.; Spector, N.L. Truncated ErbB2 receptor (p95ErbB2) is regulated by heregulin through heterodimer formation with ErbB3 yet remains sensitive to the dual EGFR/ErbB2 kinase inhibitor GW572016. Oncogene, 2004, 23(3), 646-653.
[http://dx.doi.org/10.1038/sj.onc.1207166] [PMID: 14737100]
[132]
Rodig, S.J.; Shapiro, G.I. Crizotinib, a small-molecule dual inhibitor of the c-Met and ALK receptor tyrosine kinases. Curr. Opin. Investig. Drugs, 2010, 11(12), 1477-1490.
[PMID: 21154129]
[133]
Syed, Y.Y. Ribociclib: First Global Approval. Drugs, 2017, 77(7), 799-807.
[http://dx.doi.org/10.1007/s40265-017-0742-0] [PMID: 28417244]
[134]
Mori, K.; Mostafaei, H.; Pradere, B.; Motlagh, R.S.; Quhal, F.; Laukhtina, E.; Schuettfort, V.M.; Abufaraj, M.; Karakiewicz, P.I.; Kimura, T.; Egawa, S.; Shariat, S.F. Apalutamide, enzalutamide, and darolutamide for non-metastatic castration-resistant prostate cancer: A systematic review and network meta-analysis. Int. J. Clin. Oncol., 2020, 25(11), 1892-1900.
[http://dx.doi.org/10.1007/s10147-020-01777-9] [PMID: 32924096]
[135]
Markham, A. Erdafitinib: First global approval. Drugs, 2019, 79(9), 1017-1021.
[http://dx.doi.org/10.1007/s40265-019-01142-9] [PMID: 31161538]
[136]
Syed, Y.Y. Selinexor: First global approval. Drugs, 2019, 79(13), 1485-1494.
[http://dx.doi.org/10.1007/s40265-019-01188-9] [PMID: 31429063]
[137]
Syed, Y.Y. Zanubrutinib: First approval. Drugs, 2020, 80(1), 91-97.
[http://dx.doi.org/10.1007/s40265-019-01252-4] [PMID: 31933167]
[138]
Klenk, J.; Keil, U.; Jaensch, A.; Christiansen, M.C.; Nagel, G. Changes in life expectancy 1950–2010: Contributions from age- and disease-specific mortality in selected countries. Popul. Health Metr., 2016, 14(1), 20.
[http://dx.doi.org/10.1186/s12963-016-0089-x] [PMID: 27222639]
[139]
Pan, S.Y.; Zhou, S.F.; Gao, S.H.; Yu, Z.L.; Zhang, S.F.; Tang, M.K.; Sun, J.N.; Ma, D.L.; Han, Y.F.; Fong, W.F.; Ko, K.M. New perspectives on how to discover drugs from herbal medicines: CAM’s outstanding contribution to modern therapeutics. Evid. Based Complement. Alternat. Med., 2013, 2013, 1-25.
[http://dx.doi.org/10.1155/2013/627375] [PMID: 23634172]
[140]
Schadt, E.E.; Linderman, M.D.; Sorenson, J.; Lee, L.; Nolan, G.P. Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology. Nat. Rev. Genet., 2011, 12(3), 224.
[http://dx.doi.org/10.1038/nrg2857-c2] [PMID: 21301474]
[141]
Marx, V. The big challenges of big data. Nature, 2013, 498(7453), 255-260.
[http://dx.doi.org/10.1038/498255a] [PMID: 23765498]
[142]
Zhu, H. Big data and artificial intelligence modeling for drug discovery. Annu. Rev. Pharmacol. Toxicol., 2020, 60(1), 573-589.
[http://dx.doi.org/10.1146/annurev-pharmtox-010919-023324] [PMID: 31518513]
[143]
Kim, S.; Thiessen, P.A.; Bolton, E.E.; Chen, J.; Fu, G.; Gindulyte, A.; Han, L.; He, J.; He, S.; Shoemaker, B.A.; Wang, J.; Yu, B.; Zhang, J.; Bryant, S.H. PubChem substance and compound databases. Nucleic Acids Res., 2016, 44(D1), D1202-D1213.
[http://dx.doi.org/10.1093/nar/gkv951] [PMID: 26400175]
[144]
Kim, S.; Chen, J.; Cheng, T.; Gindulyte, A.; He, J.; He, S.; Li, Q.; Shoemaker, B.A.; Thiessen, P.A.; Yu, B.; Zaslavsky, L.; Zhang, J.; Bolton, E.E. PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Res., 2021, 49(D1), D1388-D1395.
[http://dx.doi.org/10.1093/nar/gkaa971] [PMID: 33151290]
[145]
Gaulton, A.; Bellis, L.J.; Bento, A.P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J.P. ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Res., 2012, 40(D1), D1100-D1107.
[http://dx.doi.org/10.1093/nar/gkr777] [PMID: 21948594]
[146]
Irwin, J.J.; Tang, K.G.; Young, J.; Dandarchuluun, C.; Wong, B.R.; Khurelbaatar, M.; Moroz, Y.S.; Mayfield, J.; Sayle, R.A. ZINC20—A free ultralarge-scale chemical database for ligand discovery. J. Chem. Inf. Model., 2020, 60(12), 6065-6073.
[http://dx.doi.org/10.1021/acs.jcim.0c00675] [PMID: 33118813]
[147]
Gilson, M.K.; Liu, T.; Baitaluk, M.; Nicola, G.; Hwang, L.; Chong, J. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res., 2016, 44(D1), D1045-D1053.
[http://dx.doi.org/10.1093/nar/gkv1072] [PMID: 26481362]
[148]
Yang, X.; Wang, Y.; Byrne, R.; Schneider, G.; Yang, S. Concepts of artificial intelligence for computer-assisted drug discovery. Chem. Rev., 2019, 119(18), 10520-10594.
[http://dx.doi.org/10.1021/acs.chemrev.8b00728] [PMID: 31294972]
[149]
Elliott, A. The Culture of AI: Everyday Life and the Digital Revolution; Routledge, 2019.
[http://dx.doi.org/10.4324/9781315387185]
[150]
Nguyen, G.; Dlugolinsky, S.; Bobák, M.; Tran, V.; López García, Á.; Heredia, I.; Malík, P.; Hluchý, L. Machine learning and deep learning frameworks and libraries for large-scale data mining: A survey. Artif. Intell. Rev., 2019, 52(1), 77-124.
[http://dx.doi.org/10.1007/s10462-018-09679-z]
[151]
Smalley, E. AI-powered drug discovery captures pharma interest. Nat. Biotechnol., 2017, 35(7), 604-605.
[http://dx.doi.org/10.1038/nbt0717-604] [PMID: 28700560]
[152]
Dwivedi, Y.K.; Hughes, L.; Ismagilova, E.; Aarts, G.; Coombs, C.; Crick, T.; Duan, Y.; Dwivedi, R.; Edwards, J.; Eirug, A.; Galanos, V.; Ilavarasan, P.V.; Janssen, M.; Jones, P.; Kar, A.K.; Kizgin, H.; Kronemann, B.; Lal, B.; Lucini, B.; Medaglia, R.; Le Meunier-FitzHugh, K.; Le Meunier-FitzHugh, L.C.; Misra, S.; Mogaji, E.; Sharma, S.K.; Singh, J.B.; Raghavan, V.; Raman, R.; Rana, N.P.; Samothrakis, S.; Spencer, J.; Tamilmani, K.; Tubadji, A.; Walton, P.; Williams, M.D. Artificial Intelligence (AI): Multidisciplinary perspectives on emerging challenges, opportunities, and agenda for research, practice and policy. Int. J. Inf. Manage., 2021, 57, 101994.
[http://dx.doi.org/10.1016/j.ijinfomgt.2019.08.002]
[153]
Kaur, I.; Behl, T.; Aleya, L.; Rahman, H.; Kumar, A.; Arora, S.; Bulbul, I.J. Artificial intelligence as a fundamental tool in management of infectious diseases and its current implementation in COVID-19 pandemic. Environ. Sci. Pollut. Res. Int., 2021, 28(30), 40515-40532.
[http://dx.doi.org/10.1007/s11356-021-13823-8] [PMID: 34036497]
[154]
Gawriljuk, V.O.; Zin, P.P.K.; Puhl, A.C.; Zorn, K.M.; Foil, D.H.; Lane, T.R.; Hurst, B.; Tavella, T.A.; Costa, F.T.M.; Lakshmanane, P.; Bernatchez, J.; Godoy, A.S.; Oliva, G.; Siqueira-Neto, J.L.; Madrid, P.B.; Ekins, S. Machine learning models identify inhibitors of SARS-CoV-2. J. Chem. Inf. Model., 2021, 61(9), 4224-4235.
[http://dx.doi.org/10.1021/acs.jcim.1c00683] [PMID: 34387990]
[155]
Zhavoronkov, A.; Ivanenkov, Y.A.; Aliper, A.; Veselov, M.S.; Aladinskiy, V.A.; Aladinskaya, A.V.; Terentiev, V.A.; Polykovskiy, D.A.; Kuznetsov, M.D.; Asadulaev, A.; Volkov, Y.; Zholus, A.; Shayakhmetov, R.R.; Zhebrak, A.; Minaeva, L.I.; Zagribelnyy, B.A.; Lee, L.H.; Soll, R.; Madge, D.; Xing, L.; Guo, T.; Aspuru-Guzik, A. Deep learning enables rapid identification of potent DDR1 kinase inhibitors. Nat. Biotechnol., 2019, 37(9), 1038-1040.
[http://dx.doi.org/10.1038/s41587-019-0224-x] [PMID: 31477924]
[156]
Lo, Y.C.; Rensi, S.E.; Torng, W.; Altman, R.B. Machine learning in chemoinformatics and drug discovery. Drug Discov. Today, 2018, 23(8), 1538-1546.
[http://dx.doi.org/10.1016/j.drudis.2018.05.010] [PMID: 29750902]
[157]
Danishuddin; Khan, A.U. Descriptors and their selection methods in QSAR analysis: Paradigm for drug design. Drug Discov. Today, 2016, 21(8), 1291-1302.
[http://dx.doi.org/10.1016/j.drudis.2016.06.013] [PMID: 27326911]
[158]
Zefirov, N.S.; Palyulin, V.A. Fragmental Approach in QSPR. J. Chem. Inf. Comput. Sci., 2002, 42(5), 1112-1122.
[http://dx.doi.org/10.1021/ci020010e] [PMID: 12376998]
[159]
Raymond, J.W.; Willett, P. Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases. J. Comput. Aided Mol. Des., 2002, 16(1), 59-71.
[http://dx.doi.org/10.1023/A:1016387816342] [PMID: 12197666]
[160]
Hessler, G.; Baringhaus, K.H. Artificial intelligence in drug design. Molecules, 2018, 23(10), 2520.
[http://dx.doi.org/10.3390/molecules23102520] [PMID: 30279331]
[161]
Rifaioglu, A.S.; Atas, H.; Martin, M.J.; Cetin-Atalay, R.; Atalay, V.; Doğan, T. Recent applications of deep learning and machine intelligence on in silico drug discovery: Methods, tools and databases. Brief. Bioinform., 2019, 20(5), 1878-1912.
[http://dx.doi.org/10.1093/bib/bby061] [PMID: 30084866]
[162]
Tripathi, M.K.; Nath, A.; Singh, T.P.; Ethayathulla, A.S.; Kaur, P. Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. Mol. Divers., 2021, 25(3), 1439-1460.
[http://dx.doi.org/10.1007/s11030-021-10256-w] [PMID: 34159484]
[163]
RDKit. Available from: http://www.rdkit.org/ (Accessed on: Feb 15, 2022).
[164]
O’Boyle, N.M.; Banck, M.; James, C.A.; Morley, C.; Vandermeersch, T.; Hutchison, G.R. Open Babel: An open chemical toolbox. J. Cheminform., 2011, 3(1), 33.
[http://dx.doi.org/10.1186/1758-2946-3-33] [PMID: 21982300]
[165]
Helguera, A.; Combes, R.; González, M.; Cordeiro, M.N. Applications of 2D descriptors in drug design: A DRAGON tale. Curr. Top. Med. Chem., 2008, 8(18), 1628-1655.
[http://dx.doi.org/10.2174/156802608786786598] [PMID: 19075771]
[166]
Yap, C.W. PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. J. Comput. Chem., 2011, 32(7), 1466-1474.
[http://dx.doi.org/10.1002/jcc.21707] [PMID: 21425294]
[167]
Ghasemi, F.; Mehridehnavi, A.; Fassihi, A.; Pérez-Sánchez, H. Deep neural network in QSAR studies using deep belief network. Appl. Soft Comput., 2018, 62, 251-258.
[http://dx.doi.org/10.1016/j.asoc.2017.09.040]
[168]
Sanchez-Lengeling, B.; Outeiral, C.; Guimaraes, G.L.; Aspuru-Guzik, A. Optimizing distributions over molecular space. an objective-reinforced generative adversarial network for inverse-design chemistry. ChemRxiv, 2017. Available from: https://chem.rxiv.org/engage/chemrxiv/article-details/60c73d91702a9beea7189bc2
[169]
Duvenaud, D.K.; Maclaurin, D.; Iparraguirre, J.; Bombarell, R.; Hirzel, T.; Aspuru-Guzik, A.; Adams, R.P. Convolutional networks on graphs for learning molecular fingerprints. Adv. Neural Inf. Process. Syst., 2015, 2015, 28.
[170]
Senior, A.W.; Evans, R.; Jumper, J.; Kirkpatrick, J.; Sifre, L.; Green, T.; Qin, C.; Žídek, A.; Nelson, A.W.R.; Bridgland, A.; Penedones, H.; Petersen, S.; Simonyan, K.; Crossan, S.; Kohli, P.; Jones, D.T.; Silver, D.; Kavukcuoglu, K.; Hassabis, D. Improved protein structure prediction using potentials from deep learning. Nature, 2020, 577(7792), 706-710.
[http://dx.doi.org/10.1038/s41586-019-1923-7] [PMID: 31942072]
[171]
Wang, C.; Zhang, Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J. Comput. Chem., 2017, 38(3), 169-177.
[http://dx.doi.org/10.1002/jcc.24667] [PMID: 27859414]
[172]
Mayr, A.; Klambauer, G.; Unterthiner, T.; Hochreiter, S. DeepTox: Toxicity prediction using deep learning. Front. Environ. Sci., 2016, 3, 80.
[http://dx.doi.org/10.3389/fenvs.2015.00080]
[173]
Stork, C.; Chen, Y.; Šícho, M.; Kirchmair, J. Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. J. Chem. Inf. Model., 2019, 59(3), 1030-1043.
[http://dx.doi.org/10.1021/acs.jcim.8b00677] [PMID: 30624935]
[174]
Frank, E.; Hall, M.; Trigg, L.; Holmes, G.; Witten, I.H. Data mining in bioinformatics using Weka. Bioinformatics, 2004, 20(15), 2479-2481.
[http://dx.doi.org/10.1093/bioinformatics/bth261] [PMID: 15073010]
[175]
Rowe, M. An introduction to machine learning for clinicians. Acad. Med., 2019, 94(10), 1433-1436.
[176]
Baştanlar, Y.; Özuysal, M. Introduction to machine learning. Methods Mol. Biol., 2014, 1107, 105-128.
[http://dx.doi.org/10.1007/978-1-62703-748-8_7] [PMID: 24272434]
[177]
Carpenter, K.A.; Huang, X. Machine learning-based virtual screening and its applications to alzheimer’s drug discovery: A review. Curr. Pharm. Des., 2018, 24(28), 3347-3358.
[http://dx.doi.org/10.2174/1381612824666180607124038] [PMID: 29879881]
[178]
Badillo, S.; Banfai, B.; Birzele, F.; Davydov, I.I.; Hutchinson, L.; Kam-Thong, T.; Siebourg-Polster, J.; Steiert, B.; Zhang, J.D. An introduction to machine learning. Clin. Pharmacol. Ther., 2020, 107(4), 871-885.
[http://dx.doi.org/10.1002/cpt.1796] [PMID: 32128792]
[179]
Kolluri, S.; Lin, J.; Liu, R.; Zhang, Y.; Zhang, W. Machine learning and artificial intelligence in pharmaceutical research and development: A review. AAPS J., 2022, 24(1), 19.
[http://dx.doi.org/10.1208/s12248-021-00644-3] [PMID: 34984579]
[180]
LeCun, Y.; Bengio, Y.; Hinton, G. Deep learning. Nature, 2015, 521(7553), 436-444.
[http://dx.doi.org/10.1038/nature14539] [PMID: 26017442]
[181]
Lavecchia, A. Machine-learning approaches in drug discovery: Methods and applications. Drug Discov. Today, 2015, 20(3), 318-331.
[http://dx.doi.org/10.1016/j.drudis.2014.10.012] [PMID: 25448759]
[182]
Camacho, D.M.; Collins, K.M.; Powers, R.K.; Costello, J.C.; Collins, J.J. Next-generation machine learning for biological networks. Cell, 2018, 173(7), 1581-1592.
[http://dx.doi.org/10.1016/j.cell.2018.05.015] [PMID: 29887378]
[183]
Boser, B.E.; Guyon, I.M.; Vapnik, V.N. A training algorithm for optimal margin classifiers. Proceedings of the fifth annual workshop on Computational learning theory, Available from: https://dl.acm.org/doi/abs/10.1145/130385.130401 (Accessed Feb 15, 2022).
[184]
Heikamp, K.; Bajorath, J. Support vector machines for drug discovery. Expert Opin. Drug Discov., 2014, 9(1), 93-104.
[http://dx.doi.org/10.1517/17460441.2014.866943] [PMID: 24304044]
[185]
Ben-Hur, A.; Weston, J. A user’s guide to support vector machines. Methods Mol. Biol., 2010, 609, 223-239.
[186]
Patel, L.; Shukla, T.; Huang, X.; Ussery, D.W.; Wang, S. Machine learning methods in drug discovery. Molecules, 2020, 25(22), 5277.
[http://dx.doi.org/10.3390/molecules25225277] [PMID: 33198233]
[187]
Huang, S.; Cai, N.; Pacheco, P.P.; Narrandes, S.; Wang, Y.; Xu, W. Applications of support vector machine (SVM) learning in cancer genomics. Cancer Genom. Proteomics, 2018, 15(1), 41-51.
[PMID: 29275361]
[188]
Carracedo-Reboredo, P.; Liñares-Blanco, J.; Rodríguez-Fernández, N.; Cedrón, F.; Novoa, F.J.; Carballal, A.; Maojo, V.; Pazos, A.; Fernandez-Lozano, C. A review on machine learning approaches and trends in drug discovery. Comput. Struct. Biotechnol. J., 2021, 19, 4538-4558.
[http://dx.doi.org/10.1016/j.csbj.2021.08.011] [PMID: 34471498]
[189]
Gao, L.; Ye, M.; Wu, C. Cancer classification based on support vector machine optimized by particle swarm optimization and artificial bee colony. Molecules, 2017, 22(12), 2086.
[http://dx.doi.org/10.3390/molecules22122086] [PMID: 29186052]
[190]
Chao, C.F.; Horng, M.H. The construction of support vector machine classifier using the firefly algorithm. Comput. Intell. Neurosci., 2015, 2015, 1-8.
[http://dx.doi.org/10.1155/2015/212719] [PMID: 25802511]
[191]
Maltarollo, V.G.; Kronenberger, T.; Espinoza, G.Z.; Oliveira, P.R.; Honorio, K.M. Advances with support vector machines for novel drug discovery. Expert Opin. Drug Discov., 2019, 14(1), 23-33.
[http://dx.doi.org/10.1080/17460441.2019.1549033] [PMID: 30488731]
[192]
Li, Q.; Lai, L. Prediction of potential drug targets based on simple sequence properties. BMC Bioinform., 2007, 8(1), 353.
[http://dx.doi.org/10.1186/1471-2105-8-353] [PMID: 17883836]
[193]
Bakheet, T.M.; Doig, A.J. Properties and identification of human protein drug targets. Bioinformatics, 2009, 25(4), 451-457.
[http://dx.doi.org/10.1093/bioinformatics/btp002] [PMID: 19164304]
[194]
Ben-Hur, A.; Ong, C.S.; Sonnenburg, S.; Schölkopf, B.; Rätsch, G. Support vector machines and kernels for computational biology. PLOS Comput. Biol., 2008, 4(10), e1000173.
[http://dx.doi.org/10.1371/journal.pcbi.1000173] [PMID: 18974822]
[195]
Wang, H.W.; Lin, Y.C.; Pai, T.W.; Chang, H.T. Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J. Biomed. Biotechnol., 2011, 2011, 1-12.
[http://dx.doi.org/10.1155/2011/432830] [PMID: 21876642]
[196]
Burbidge, R.; Trotter, M.; Buxton, B.; Holden, S. Drug design by machine learning: Support vector machines for pharmaceutical data analysis. Comput. Chem., 2001, 26(1), 5-14.
[http://dx.doi.org/10.1016/S0097-8485(01)00094-8] [PMID: 11765851]
[197]
Sun, G.; Fan, T.; Sun, X.; Hao, Y.; Cui, X.; Zhao, L.; Ren, T.; Zhou, Y.; Zhong, R.; Peng, Y. In silico prediction of O6-Methylguanine-DNA methyltransferase inhibitory potency of base analogs with QSAR and machine learning methods. Molecules, 2018, 23(11), 2892.
[http://dx.doi.org/10.3390/molecules23112892] [PMID: 30404161]
[198]
Zhao, M.; Wang, L.; Zheng, L.; Zhang, M.; Qiu, C.; Zhang, Y.; Du, D.; Niu, B. 2D-QSAR and 3D-QSAR analyses for EGFR inhibitors. BioMed Res. Int., 2017, 2017, 1-11.
[http://dx.doi.org/10.1155/2017/4649191] [PMID: 28630865]
[199]
Lind, P.; Maltseva, T. Support vector machines for the estimation of aqueous solubility. J. Chem. Inf. Comput. Sci., 2003, 43(6), 1855-1859.
[http://dx.doi.org/10.1021/ci034107s] [PMID: 14632433]
[200]
Cheng, T.; Li, Q.; Wang, Y.; Bryant, S.H. Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection. J. Chem. Inf. Model., 2011, 51(2), 229-236.
[http://dx.doi.org/10.1021/ci100364a] [PMID: 21214224]
[201]
Sharma, A.; Varadwaj, P.K.; Kumar, R. A prediction model for oral bioavailability of drugs using physicochemical properties by support vector machine. J. Nat. Sci. Biol. Med., 2011, 2(2), 168-173.
[http://dx.doi.org/10.4103/0976-9668.92325] [PMID: 22346230]
[202]
Korkmaz, S.; Zararsiz, G.; Goksuluk, D. Drug/nondrug classification using Support Vector Machines with various feature selection strategies. Comput. Methods Programs Biomed., 2014, 117(2), 51-60.
[http://dx.doi.org/10.1016/j.cmpb.2014.08.009] [PMID: 25224081]
[203]
Jeon, J.; Nim, S.; Teyra, J.; Datti, A.; Wrana, J.L.; Sidhu, S.S.; Moffat, J.; Kim, P.M. A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. Genome Med., 2014, 6(7), 57.
[http://dx.doi.org/10.1186/s13073-014-0057-7] [PMID: 25165489]
[204]
Chen, X.; Xie, W.; Yang, Y.; Hua, Y.; Xing, G.; Liang, L.; Deng, C.; Wang, Y.; Fan, Y.; Liu, H.; Lu, T.; Chen, Y.; Zhang, Y. Discovery of dual FGFR4 and EGFR inhibitors by machine learning and biological evaluation. J. Chem. Inf. Model., 2020, 60(10), 4640-4652.
[http://dx.doi.org/10.1021/acs.jcim.0c00652] [PMID: 32926776]
[205]
Tong, Z.; Zhou, Y.; Wang, J. Identifying potential drug targets in hepatocellular carcinoma based on network analysis and one-class support vector machine. Sci. Rep., 2019, 9(1), 10442.
[http://dx.doi.org/10.1038/s41598-019-46540-x] [PMID: 31320657]
[206]
Fang, J.; Yang, R.; Gao, L.; Zhou, D.; Yang, S.; Liu, A.; Du, G. Predictions of BuChE inhibitors using support vector machine and naive Bayesian classification techniques in drug discovery. J. Chem. Inf. Model., 2013, 53(11), 3009-3020.
[http://dx.doi.org/10.1021/ci400331p] [PMID: 24144102]
[207]
Kong, Y.; Qu, D.; Chen, X.; Gong, Y.N.; Yan, A. Self-organizing map (SOM) and support vector machine (SVM) models for the prediction of human epidermal growth factor receptor (EGFR/ErbB-1) Inhibitors. Comb. Chem. High Throughput Screen., 2016, 19(5), 400-411.
[http://dx.doi.org/10.2174/1386207319666160414105044] [PMID: 27074760]
[208]
Wang, L.; Wang, M.; Yan, A.; Dai, B. Using self-organizing map (SOM) and support vector machine (SVM) for classification of selectivity of ACAT inhibitors. Mol. Divers., 2013, 17(1), 85-96.
[http://dx.doi.org/10.1007/s11030-012-9404-z] [PMID: 23124952]
[209]
Abbasi-Radmoghaddam, Z.; Riahi, S.; Gharaghani, S.; Mohammadi-Khanaposhtanai, M. Design of potential anti-tumor PARP-1 inhibitors by QSAR and molecular modeling studies. Mol. Divers., 2021, 25(1), 263-277.
[http://dx.doi.org/10.1007/s11030-020-10063-9] [PMID: 32140890]
[210]
Lian, W.; Fang, J.; Li, C.; Pang, X.; Liu, A.L.; Du, G.H. Discovery of influenza a virus neuraminidase inhibitors using support vector machine and naïve bayesian models. Mol. Divers., 2016, 20(2), 439-451.
[http://dx.doi.org/10.1007/s11030-015-9641-z] [PMID: 26689205]
[211]
Romero-Molina, S.; Ruiz-Blanco, Y.B.; Harms, M.; Münch, J.; Sanchez-Garcia, E. PPI-Detect: A support vector machine model for sequence-based prediction of protein-protein interactions. J. Comput. Chem., 2019, 40(11), 1233-1242.
[http://dx.doi.org/10.1002/jcc.25780] [PMID: 30768790]
[212]
Sugaya, N.; Ikeda, K. Assessing the druggability of protein-protein interactions by a supervised machine-learning method. BMC Bioinform., 2009, 10(1), 263.
[http://dx.doi.org/10.1186/1471-2105-10-263] [PMID: 19703312]
[213]
Cui, G.; Fang, C.; Han, K. Prediction of protein-protein interactions between viruses and human by an SVM model. BMC Bioinform., 2012, 13(Suppl. 7), S5.
[http://dx.doi.org/10.1186/1471-2105-13-S7-S5] [PMID: 22595002]
[214]
Uddin, S.; Khan, A.; Hossain, M.E.; Moni, M.A. Comparing different supervised machine learning algorithms for disease prediction. BMC Med. Inform. Decis. Mak., 2019, 19(1), 281.
[http://dx.doi.org/10.1186/s12911-019-1004-8] [PMID: 31864346]
[215]
Quinlan, J.R. Learning efficient classification procedures and their application to chess end games. In: Machine learning; Springer, 1983; pp. 463-482.
[216]
Breiman, L. Random Forests. Mach. Learn., 2001, 45(1), 5-32.
[http://dx.doi.org/10.1023/A:1010933404324]
[217]
Sarica, A.; Cerasa, A.; Quattrone, A. Random forest algorithm for the classification of neuroimaging data in Alzheimer’s Disease: A systematic review. Front. Aging Neurosci., 2017, 9, 329.
[http://dx.doi.org/10.3389/fnagi.2017.00329] [PMID: 29056906]
[218]
Wei, M.; Zhang, X.; Pan, X.; Wang, B.; Ji, C.; Qi, Y.; Zhang, J.Z.H. HobPre: Accurate prediction of human oral bioavailability for small molecules. J. Cheminform., 2022, 14(1), 1.
[http://dx.doi.org/10.1186/s13321-021-00580-6] [PMID: 34991690]
[219]
Lind, A.P.; Anderson, P.C. Predicting drug activity against cancer cells by random forest models based on minimal genomic information and chemical properties. PLoS One, 2019, 14(7), e0219774.
[http://dx.doi.org/10.1371/journal.pone.0219774] [PMID: 31295321]
[220]
Ryu, J.Y.; Lee, J.H.; Lee, B.H.; Song, J.S.; Ahn, S.; Oh, K.-S. PredMS: A random forest model for predicting metabolic stability of drug candidates in human liver microsomes. Bioinforma. Oxf. Engl., 2021, 2021, btab547.
[221]
Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J.C.; Sheridan, R.P.; Feuston, B.P. Random forest: A classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Comput. Sci., 2003, 43(6), 1947-1958.
[http://dx.doi.org/10.1021/ci034160g] [PMID: 14632445]
[222]
Singh, H.; Singh, S.; Singla, D.; Agarwal, S.M.; Raghava, G.P.S. QSAR based model for discriminating EGFR inhibitors and non-inhibitors using Random forest. Biol. Direct, 2015, 10(1), 10.
[http://dx.doi.org/10.1186/s13062-015-0046-9] [PMID: 25880749]
[223]
Shi, H.; Liu, S.; Chen, J.; Li, X.; Ma, Q.; Yu, B. Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure. Genomics, 2019, 111(6), 1839-1852.
[http://dx.doi.org/10.1016/j.ygeno.2018.12.007] [PMID: 30550813]
[224]
Rahman, R.; Dhruba, S.R.; Ghosh, S.; Pal, R. Functional random forest with applications in dose-response predictions. Sci. Rep., 2019, 9(1), 1628.
[http://dx.doi.org/10.1038/s41598-018-38231-w] [PMID: 30733524]
[225]
Kouchaki, S.; Yang, Y.; Lachapelle, A.; Walker, T.M.; Walker, A.S.; Peto, T.E.A.; Crook, D.W.; Clifton, D.A. Multi-label random forest model for tuberculosis drug resistance classification and mutation ranking. Front. Microbiol., 2020, 11, 667.
[http://dx.doi.org/10.3389/fmicb.2020.00667] [PMID: 32390972]
[226]
Hu, J.; Li, Y.; Yang, J.Y.; Shen, H.B.; Yu, D.J. GPCR–drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure. Comput. Biol. Chem., 2016, 60, 59-71.
[http://dx.doi.org/10.1016/j.compbiolchem.2015.11.007] [PMID: 26674225]
[227]
Ubels, J.; Schaefers, T.; Punt, C.; Guchelaar, H.J.; de Ridder, J. RAINFOREST: A random forest approach to predict treatment benefit in data from (failed) clinical drug trials. Bioinformatics, 2020, 36(Suppl. 2), i601-i609.
[http://dx.doi.org/10.1093/bioinformatics/btaa799] [PMID: 33381829]
[228]
Wani, M.A.; Garg, P.; Roy, K.K. Machine learning-enabled predictive modeling to precisely identify the antimicrobial peptides. Med. Biol. Eng. Comput., 2021, 59(11-12), 2397-2408.
[http://dx.doi.org/10.1007/s11517-021-02443-6] [PMID: 34632545]
[229]
Zhou, Y.; Li, S.; Zhao, Y.; Guo, M.; Liu, Y.; Li, M.; Wen, Z. Quantitative Structure–Activity Relationship (QSAR) model for the severity prediction of drug-induced rhabdomyolysis by using random forest. Chem. Res. Toxicol., 2021, 34(2), 514-521.
[http://dx.doi.org/10.1021/acs.chemrestox.0c00347] [PMID: 33393765]
[230]
Quinlan, J.R. Induction of decision trees. Mach. Learn., 1986, 1(1), 81-106.
[http://dx.doi.org/10.1007/BF00116251]
[231]
Prasanthi, L.S.; Kumar, R.K. ID3 and its applications in generation of decision trees across various domains-survey. Int. J. Comput. Sci. Inf. Technol., 2015, 2015, 5353-5357.
[232]
Rehman, O.; Zhuang, H.; Muhamed Ali, A.; Ibrahim, A.; Li, Z. Validation of miRNAs as breast cancer biomarkers with a machine learning approach. Cancers (Basel), 2019, 11(3), 431.
[http://dx.doi.org/10.3390/cancers11030431] [PMID: 30917548]
[233]
Breiman, L. Technical note: Some properties of splitting criteria. Mach. Learn., 1996, 24(1), 41-47.
[http://dx.doi.org/10.1007/BF00117831]
[234]
Maheswari, S.; Pitchai, R. Heart disease prediction system using decision tree and naive bayes algorithm. Curr. Med. Imaging Rev., 2019, 15(8), 712-717.
[http://dx.doi.org/10.2174/1573405614666180322141259] [PMID: 32008540]
[235]
Yücebaş, S.C.; Aydın Son, Y. A prostate cancer model build by a novel SVM-ID3 hybrid feature selection method using both genotyping and phenotype data from dbGaP. PLoS One, 2014, 9(3), e91404.
[http://dx.doi.org/10.1371/journal.pone.0091404] [PMID: 24651484]
[236]
Che, D.; Liu, Q.; Rasheed, K.; Tao, X. Decision tree and ensemble learning algorithms with their applications in bioinformatics. Adv. Exp. Med. Biol., 2011, 696, 191-199.
[http://dx.doi.org/10.1007/978-1-4419-7046-6_19] [PMID: 21431559]
[237]
Li, B.; Hu, L.; Xue, Y.; Yang, M.; Huang, L.; Zhang, Z.; Liu, J.; Deng, G. Prediction of matrix metal proteinases-12 inhibitors by machine learning approaches. J. Biomol. Struct. Dyn., 2019, 37(10), 2627-2640.
[http://dx.doi.org/10.1080/07391102.2018.1492460] [PMID: 30051748]
[238]
Reddy, G.S.; Chittineni, S. Entropy based C4.5-SHO algorithm with information gain optimization in data mining. PeerJ Comput. Sci., 2021, 7, e424.
[http://dx.doi.org/10.7717/peerj-cs.424] [PMID: 33954229]
[239]
Breiman, L.; Friedman, J.; Olshen, R.; Stone, C. Classification and Regression Trees, Wadsworth International Group, Belmont, California, USA, 1984; BP Roe et al. Boosted Decision Trees as an Alternative to Artificial Neural Networks for Particle Identification. Nucl. Instrum. Meth. A, 2005, 543, 10-1016.
[240]
Lin, X.; Li, X.; Lin, X. A review on applications of computational methods in drug screening and design. Molecules, 2020, 25(6), 1375.
[http://dx.doi.org/10.3390/molecules25061375] [PMID: 32197324]
[241]
Nigsch, F.; Bender, A.; Jenkins, J.L.; Mitchell, J.B.O. Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics. J. Chem. Inf. Model., 2008, 48(12), 2313-2325.
[http://dx.doi.org/10.1021/ci800079x] [PMID: 19055411]
[242]
Bosc, N.; Felix, E.; Arcila, R.; Mendez, D.; Saunders, M.R.; Green, D.V.S.; Ochoada, J.; Shelat, A.A.; Martin, E.J.; Iyer, P.; Engkvist, O.; Verras, A.; Duffy, J.; Burrows, J.; Gardner, J.M.F.; Leach, A.R. MAIP: A web service for predicting blood‐stage malaria inhibitors. J. Cheminform., 2021, 13(1), 13.
[http://dx.doi.org/10.1186/s13321-021-00487-2] [PMID: 33618772]
[243]
Madhukar, N.S.; Khade, P.K.; Huang, L.; Gayvert, K.; Galletti, G.; Stogniew, M.; Allen, J.E.; Giannakakou, P.; Elemento, O. A Bayesian machine learning approach for drug target identification using diverse data types. Nat. Commun., 2019, 10(1), 5221.
[http://dx.doi.org/10.1038/s41467-019-12928-6] [PMID: 31745082]
[244]
Zheng, M.; Liu, Z.; Yan, X.; Ding, Q.; Gu, Q.; Xu, J. LBVS: An online platform for ligand-based virtual screening using publicly accessible databases. Mol. Divers., 2014, 18(4), 829-840.
[http://dx.doi.org/10.1007/s11030-014-9545-3] [PMID: 25182364]
[245]
Li, L.; Koh, C.C.; Reker, D.; Brown, J.B.; Wang, H.; Lee, N.K.; Liow, H.; Dai, H.; Fan, H.M.; Chen, L.; Wei, D.Q. Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees. Sci. Rep., 2019, 9(1), 7703.
[http://dx.doi.org/10.1038/s41598-019-43125-6] [PMID: 31118426]
[246]
Zhang, H.; Kang, Y.L.; Zhu, Y.Y.; Zhao, K.X.; Liang, J.Y.; Ding, L.; Zhang, T.G.; Zhang, J. Novel naïve Bayes classification models for predicting the chemical Ames mutagenicity. Toxicol. In Vitro, 2017, 41, 56-63.
[http://dx.doi.org/10.1016/j.tiv.2017.02.016] [PMID: 28232239]
[247]
Zhang, H.; Yu, P.; Ren, J.X.; Li, X.B.; Wang, H.L.; Ding, L.; Kong, W.B. Development of novel prediction model for drug-induced mitochondrial toxicity by using naïve Bayes classifier method. Food Chem. Toxicol., 2017, 110, 122-129.
[http://dx.doi.org/10.1016/j.fct.2017.10.021] [PMID: 29042293]
[248]
Zhang, H.; Ma, J.X.; Liu, C.T.; Ren, J.X.; Ding, L. Development and evaluation of in silico prediction model for drug-induced respiratory toxicity by using naïve Bayes classifier method. Food Chem. Toxicol., 2018, 121, 593-603.
[http://dx.doi.org/10.1016/j.fct.2018.09.051] [PMID: 30261216]
[249]
Shi, H.; Tian, S.; Li, Y.; Li, D.; Yu, H.; Zhen, X.; Hou, T. Absorption, distribution, metabolism, excretion, and toxicity evaluation in drug discovery. 14. prediction of human pregnane X receptor activators by using naive bayesian classification technique. Chem. Res. Toxicol., 2015, 28(1), 116-125.
[http://dx.doi.org/10.1021/tx500389q] [PMID: 25495542]
[250]
Perryman, A.L.; Patel, J.S.; Russo, R.; Singleton, E.; Connell, N.; Ekins, S.; Freundlich, J.S. Naïve bayesian models for vero cell cytotoxicity. Pharm. Res., 2018, 35(9), 170.
[http://dx.doi.org/10.1007/s11095-018-2439-9] [PMID: 29959603]
[251]
Wei, Y.; Li, W.; Du, T.; Hong, Z.; Lin, J. Targeting HIV/HCV coinfection using a machine learning-based multiple quantitative structure-activity relationships (multiple QSAR) method. Int. J. Mol. Sci., 2019, 20(14), 3572.
[http://dx.doi.org/10.3390/ijms20143572] [PMID: 31336592]
[252]
Cover, T.; Hart, P. Nearest neighbor pattern classification. IEEE Trans. Inf. Theory, 1967, 13(1), 21-27.
[http://dx.doi.org/10.1109/TIT.1967.1053964]
[253]
Huang, W.L.; Chen, H.M.; Hwang, S.F.; Ho, S.Y. Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method. Biosystems, 2007, 90(2), 405-413.
[http://dx.doi.org/10.1016/j.biosystems.2006.10.004] [PMID: 17140725]
[254]
Kamath, S.D.; Bhat, R.A.; Ray, S.; Mahato, K.K. Autofluorescence of normal, benign, and malignant ovarian tissues: A pilot study. Photomed. Laser Surg., 2009, 27(2), 325-335.
[http://dx.doi.org/10.1089/pho.2008.2261] [PMID: 18800945]
[255]
Ajmani, S.; Jadhav, K.; Kulkarni, S.A. Three-dimensional QSAR using the k-nearest neighbor method and its interpretation. J. Chem. Inf. Model., 2006, 46(1), 24-31.
[http://dx.doi.org/10.1021/ci0501286] [PMID: 16426036]
[256]
Shen, M.; Xiao, Y.; Golbraikh, A.; Gombar, V.K.; Tropsha, A. Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates. J. Med. Chem., 2003, 46(14), 3013-3020.
[http://dx.doi.org/10.1021/jm020491t] [PMID: 12825940]
[257]
Kauffman, G.W.; Jurs, P.C. QSAR and k-nearest neighbor classification analysis of selective cyclooxygenase-2 inhibitors using topologically-based numerical descriptors. J. Chem. Inf. Comput. Sci., 2001, 41(6), 1553-1560.
[http://dx.doi.org/10.1021/ci010073h] [PMID: 11749582]
[258]
Chavan, S.; Abdelaziz, A.; Wiklander, J.G.; Nicholls, I.A. A k-nearest neighbor classification of hERG K+ channel blockers. J. Comput. Aided Mol. Des., 2016, 30(3), 229-236.
[http://dx.doi.org/10.1007/s10822-016-9898-z] [PMID: 26860111]
[259]
Arian, R.; Hariri, A.; Mehridehnavi, A.; Fassihi, A.; Ghasemi, F. Protein kinase inhibitors’ classification using K-Nearest neighbor algorithm. Comput. Biol. Chem., 2020, 86, 107269.
[http://dx.doi.org/10.1016/j.compbiolchem.2020.107269] [PMID: 32413830]
[260]
Jing, Y.; Bian, Y.; Hu, Z.; Wang, L.; Xie, X.Q.S. Deep Learning for drug design: An artificial intelligence paradigm for drug discovery in the big data era. AAPS J., 2018, 20(3), 58.
[http://dx.doi.org/10.1208/s12248-018-0210-0] [PMID: 29603063]
[261]
McCulloch, W.; Pitts, W. A logical calculus of the ideas immanent in nervous activity. Bull. Math. Biol., 1990, 52(1-2), 99-115.
[http://dx.doi.org/10.1016/S0092-8240(05)80006-0] [PMID: 2185863]
[262]
Angermueller, C.; Pärnamaa, T.; Parts, L.; Stegle, O. Deep learning for computational biology. Mol. Syst. Biol., 2016, 12(7), 878.
[http://dx.doi.org/10.15252/msb.20156651] [PMID: 27474269]
[263]
Kimber, T.B.; Chen, Y.; Volkamer, A. Deep learning in virtual screening: Recent applications and developments. Int. J. Mol. Sci., 2021, 22(9), 4435.
[http://dx.doi.org/10.3390/ijms22094435] [PMID: 33922714]
[264]
Hiller, S.A.; Golender, V.E.; Rosenblit, A.B.; Rastrigin, L.A.; Glaz, A.B. Cybernetic methods of drug design. I. Statement of the problem—The perceptron approach. Comput. Biomed. Res., 1973, 6(5), 411-421.
[http://dx.doi.org/10.1016/0010-4809(73)90074-8] [PMID: 4747104]
[265]
Ogami, C.; Tsuji, Y.; Seki, H.; Kawano, H.; To, H.; Matsumoto, Y.; Hosono, H. An artificial neural network−pharmacokinetic model and its interpretation using Shapley additive explanations. CPT Pharmacometr. Syst. Pharmacol., 2021, 10(7), 760-768.
[http://dx.doi.org/10.1002/psp4.12643] [PMID: 33955705]
[266]
Wang, S.; Di, J.; Wang, D.; Dai, X.; Hua, Y.; Gao, X.; Zheng, A.; Gao, J. State-of-the-Art review of artificial neural networks to predict, characterize and optimize pharmaceutical formulation. Pharmaceutics, 2022, 14(1), 183.
[http://dx.doi.org/10.3390/pharmaceutics14010183] [PMID: 35057076]
[267]
Szegedy, C.; Liu, W.; Jia, Y.; Sermanet, P.; Reed, S.; Anguelov, D.; Erhan, D.; Vanhoucke, V.; Rabinovich, A. Going Deep. Convolut., 2015, 2015, 7298594.
[http://dx.doi.org/10.1109/CVPR.2015.7298594]
[268]
Hu, S.; Xia, D.; Su, B.; Chen, P.; Wang, B.; Li, J. A convolutional neural network system to discriminate drug-target interactions. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 2021, 18(4), 1315-1324.
[http://dx.doi.org/10.1109/TCBB.2019.2940187] [PMID: 31514149]
[269]
Xu, X.; Xuan, P.; Zhang, T.; Chen, B.; Sheng, N. Inferring drug-target interactions based on random walk and convolutional neural network. IEEE/ACM Trans. Comput. Biol. Bioinform., 2021, 2021 [Epub ahead of print]
[270]
Shim, J.; Hong, Z.Y.; Sohn, I.; Hwang, C. Prediction of drug–target binding affinity using similarity-based convolutional neural network. Sci. Rep., 2021, 11(1), 4416.
[http://dx.doi.org/10.1038/s41598-021-83679-y] [PMID: 33627791]
[271]
Xuan, P.; Ye, Y.; Zhang, T.; Zhao, L.; Sun, C. Convolutional neural network and bidirectional long short-term memory-based method for predicting drug–disease associations. Cells, 2019, 8(7), 705.
[http://dx.doi.org/10.3390/cells8070705] [PMID: 31336774]
[272]
Zhao, H.; Li, Y.; Wang, J. A convolutional neural network and graph convolutional network based method for predicting the classification of anatomical therapeutic chemicals. Bioinform. Oxf. Engl., 2021, 2021, btab204.
[273]
Chen, J.; Si, Y.W.; Un, C.W.; Siu, S.W.I. Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network. J. Cheminform., 2021, 13(1), 93.
[http://dx.doi.org/10.1186/s13321-021-00570-8] [PMID: 34838140]
[274]
Li, S.; Zhang, L.; Feng, H.; Meng, J.; Xie, D.; Yi, L.; Arkin, I.T.; Liu, H. MutagenPred-GCNNs: A graph convolutional neural network-based classification model for mutagenicity prediction with data-driven molecular fingerprints. Interdiscip. Sci., 2021, 13(1), 25-33.
[http://dx.doi.org/10.1007/s12539-020-00407-2] [PMID: 33506363]
[275]
Ragoza, M.; Hochuli, J.; Idrobo, E.; Sunseri, J.; Koes, D.R. Protein–ligand scoring with convolutional neural networks. J. Chem. Inf. Model., 2017, 57(4), 942-957.
[http://dx.doi.org/10.1021/acs.jcim.6b00740] [PMID: 28368587]
[276]
Esteva, A.; Kuprel, B.; Novoa, R.A.; Ko, J.; Swetter, S.M.; Blau, H.M.; Thrun, S. Dermatologist-level classification of skin cancer with deep neural networks. Nature, 2017, 542(7639), 115-118.
[http://dx.doi.org/10.1038/nature21056] [PMID: 28117445]
[277]
Shameer, K.; Johnson, K.W.; Yahi, A.; Miotto, R.; Li, L.; Ricks, D.; Jebakaran, J.; Kovatch, P.; Sengupta, P.P.; Gelijns, S.; Moskovitz, A.; Darrow, B.; David, D.L.; Kasarskis, A.; Tatonetti, N.P.; Pinney, S.; Dudley, J.T. Predictive modeling of hospital readmission rates using electronic medical record-wide machine learning: A case-study using mount sinai heart failure cohort. Pac. Symp. Biocomput., 2017, 22, 276-287.
[http://dx.doi.org/10.1142/9789813207813_0027] [PMID: 27896982]
[278]
Baskin, I.I.; Winkler, D.; Tetko, I.V. A renaissance of neural networks in drug discovery. Expert Opin. Drug Discov., 2016, 11(8), 785-795.
[http://dx.doi.org/10.1080/17460441.2016.1201262] [PMID: 27295548]
[279]
Mouchlis, V.D.; Afantitis, A.; Serra, A.; Fratello, M.; Papadiamantis, A.G.; Aidinis, V.; Lynch, I.; Greco, D.; Melagraki, G. Advances in de novo drug design: From conventional to machine learning methods. Int. J. Mol. Sci., 2021, 22(4), 1676.
[http://dx.doi.org/10.3390/ijms22041676] [PMID: 33562347]
[280]
Ruiz Puentes, P.; Valderrama, N.; González, C.; Daza, L.; Muñoz-Camargo, C.; Cruz, J.C.; Arbeláez, P. PharmaNet: Pharmaceutical discovery with deep recurrent neural networks. PLoS One, 2021, 16(4), e0241728.
[http://dx.doi.org/10.1371/journal.pone.0241728] [PMID: 33901196]
[281]
Lusci, A.; Pollastri, G.; Baldi, P. Deep architectures and deep learning in chemoinformatics: The prediction of aqueous solubility for drug-like molecules. J. Chem. Inf. Model., 2013, 53(7), 1563-1575.
[http://dx.doi.org/10.1021/ci400187y] [PMID: 23795551]
[282]
Kebalepile, M.M.; Dzikiti, L.N.; Voyi, K. Supervised kohonen self-organizing maps of acute asthma from air pollution exposure. Int. J. Environ. Res. Public Health, 2021, 18(21), 11071.
[http://dx.doi.org/10.3390/ijerph182111071] [PMID: 34769590]
[283]
Jayaraj, P.B.; Sanjay, S.; Raja, K.; Gopakumar, G.; Jaleel, U.C. Ligand based virtual screening using self-organizing maps. Protein J., 2022, 41(1), 44-54.
[http://dx.doi.org/10.1007/s10930-021-10030-9] [PMID: 35022993]
[284]
Schneider, G.; Schneider, P. Macromolecular target prediction by self-organizing feature maps. Expert Opin. Drug Discov., 2017, 12(3), 271-277.
[http://dx.doi.org/10.1080/17460441.2017.1274727] [PMID: 27997811]
[285]
Reker, D.; Rodrigues, T.; Schneider, P.; Schneider, G. Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. Proc. Natl. Acad. Sci. USA, 2014, 111(11), 4067-4072.
[http://dx.doi.org/10.1073/pnas.1320001111] [PMID: 24591595]
[286]
Schneider, P.; Tanrikulu, Y.; Schneider, G. Self-organizing maps in drug discovery: Compound library design, scaffold-hopping, repurposing. Curr. Med. Chem., 2009, 16(3), 258-266.
[http://dx.doi.org/10.2174/092986709787002655] [PMID: 19149576]
[287]
Otaki, J.M.; Mori, A.; Itoh, Y.; Nakayama, T.; Yamamoto, H. Alignment-free classification of G-protein-coupled receptors using self-organizing maps. J. Chem. Inf. Model., 2006, 46(3), 1479-1490.
[http://dx.doi.org/10.1021/ci050382y] [PMID: 16711767]
[288]
Panchal, G.; Ganatra, A.; Kosta, Y.P.; Panchal, D. Behaviour analysis of multilayer perceptronswith multiple hidden neurons and hidden layers. Int. J. Comput. Theory Eng., 2011, 3, 332-337.
[http://dx.doi.org/10.7763/IJCTE.2011.V3.328]
[289]
Pal, S.K.; Mitra, S. Multilayer perceptron, fuzzy sets, and classification. IEEE Trans. Neural Netw., 1992, 3(5), 683-697.
[http://dx.doi.org/10.1109/72.159058] [PMID: 18276468]
[290]
Dara, S.; Dhamercherla, S.; Jadav, S.S.; Babu, C.M.; Ahsan, M.J. Machine learning in drug discovery: A review. Artif. Intell. Rev., 2021, 2021, 1-53.
[PMID: 34393317]
[291]
Altalib, M.K.; Salim, N. Similarity-based virtual screen using enhanced siamese multi-layer perceptron. Molecules, 2021, 26(21), 6669.
[http://dx.doi.org/10.3390/molecules26216669] [PMID: 34771076]
[292]
Gómez-Bombarelli, R.; Wei, J.N.; Duvenaud, D.; Hernández-Lobato, J.M.; Sánchez-Lengeling, B.; Sheberla, D.; Aguilera-Iparraguirre, J.; Hirzel, T.D.; Adams, R.P.; Aspuru-Guzik, A. Automatic chemical design using a data-driven continuous representation of molecules. ACS Cent. Sci., 2018, 4(2), 268-276.
[http://dx.doi.org/10.1021/acscentsci.7b00572] [PMID: 29532027]
[293]
Carkli Yavuz, B.; Yurtay, N.; Ozkan, O. Prediction of protein secondary structure with clonal selection algorithm and multilayer perceptron. IEEE Access, 2018, 6, 45256-45261.
[http://dx.doi.org/10.1109/ACCESS.2018.2864665]
[294]
Kramer, M.A. Nonlinear principal component analysis using autoassociative neural networks. AIChE J., 1991, 37(2), 233-243.
[http://dx.doi.org/10.1002/aic.690370209]
[295]
Nguyen, L.H.; Holmes, S. Ten quick tips for effective dimensionality reduction. PLOS Comput. Biol., 2019, 15(6), e1006907.
[http://dx.doi.org/10.1371/journal.pcbi.1006907] [PMID: 31220072]
[296]
Farahnakian, F.; Heikkonen, J. A Deep Auto-Encoder Based Approach for Intrusion Detection System; IEEE, 2018, pp. 178-183.
[297]
Kingma, D.P.; Welling, M. Auto-encoding variational bayes. ArXiv, 2014, 2014, 13126114.
[298]
Peng, J.; Li, J.; Shang, X. A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. BMC Bioinformatics, 2020, 21(Suppl. 13), 394.
[http://dx.doi.org/10.1186/s12859-020-03677-1] [PMID: 32938374]
[299]
Vincent, P.; Larochelle, H.; Bengio, Y.; Manzagol, P-A. Extracting and composing robust features with denoising autoencoders. Dimesions, 2008, 2008, 1096-1103.
[http://dx.doi.org/10.1145/1390156.1390294]
[300]
Hu, Q.; Feng, M.; Lai, L.; Pei, J. Prediction of drug-likeness using deep autoencoder neural networks. Front. Genet., 2018, 9, 585.
[http://dx.doi.org/10.3389/fgene.2018.00585] [PMID: 30538725]
[301]
Carpenter, K.A.; Cohen, D.S.; Jarrell, J.T.; Huang, X. Deep learning and virtual drug screening. Future Med. Chem., 2018, 10(21), 2557-2567.
[http://dx.doi.org/10.4155/fmc-2018-0314] [PMID: 30288997]
[302]
Gallego, V.; Naveiro, R.; Roca, C.; Ríos Insua, D.; Campillo, N.E. AI in drug development: A multidisciplinary perspective. Mol. Divers., 2021, 25(3), 1461-1479.
[http://dx.doi.org/10.1007/s11030-021-10266-8] [PMID: 34251580]
[303]
Jolliffe, I.T.; Cadima, J. Principal component analysis: A review and recent developments. Philos. Trans.- Royal Soc., Math. Phys. Eng. Sci., 2016, 374(2065), 20150202.
[http://dx.doi.org/10.1098/rsta.2015.0202] [PMID: 26953178]
[304]
Wenderski, T.A.; Stratton, C.F.; Bauer, R.A.; Kopp, F.; Tan, D.S. Principal component analysis as a tool for library design: A case study investigating natural products, brand-name drugs, natural product-like libraries, and drug-like libraries. Methods Mol. Biol., 2015, 1263, 225-242.
[http://dx.doi.org/10.1007/978-1-4939-2269-7_18] [PMID: 25618349]
[305]
Du, Q.S.; Wang, S.Q.; Xie, N.Z.; Wang, Q.Y.; Huang, R.B.; Chou, K.C. 2L-PCA: A two-level principal component analyzer for quantitative drug design and its applications. Oncotarget, 2017, 8(41), 70564-70578.
[http://dx.doi.org/10.18632/oncotarget.19757] [PMID: 29050302]
[306]
Owen, J.R.; Nabney, I.T.; Medina-Franco, J.L.; López-Vallejo, F. Visualization of molecular fingerprints. J. Chem. Inf. Model., 2011, 51(7), 1552-1563.
[http://dx.doi.org/10.1021/ci1004042] [PMID: 21696145]
[307]
Gao, H.; Williams, C.; Labute, P.; Bajorath, J. Binary quantitative structure-activity relationship (QSAR) analysis of estrogen receptor ligands. J. Chem. Inf. Comput. Sci., 1999, 39(1), 164-168.
[http://dx.doi.org/10.1021/ci980140g] [PMID: 10094611]
[308]
Taguchi, Y.; Iwadate, M.; Umeyama, H. Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease. BMC Bioinform., 2015, 16(1), 139.
[http://dx.doi.org/10.1186/s12859-015-0574-4] [PMID: 25925353]
[309]
Nedyalkova, M.; Madurga, S.; Simeonov, V. Combinatorial K-Means Clustering as a Machine Learning Tool Applied to Diabetes Mellitus Type 2. Int. J. Environ. Res. Public Health, 2021, 18(4), 1919.
[http://dx.doi.org/10.3390/ijerph18041919] [PMID: 33671157]
[310]
Popova, M.; Isayev, O.; Tropsha, A. Deep reinforcement learning for de novo drug design. Sci. Adv., 2018, 4(7), eaap7885.
[http://dx.doi.org/10.1126/sciadv.aap7885] [PMID: 30050984]
[311]
Pereira, T.; Abbasi, M.; Ribeiro, B.; Arrais, J.P. Diversity oriented Deep Reinforcement Learning for targeted molecule generation. J. Cheminform., 2021, 13(1), 21.
[http://dx.doi.org/10.1186/s13321-021-00498-z] [PMID: 33750461]
[312]
Dankers, F.J.W.M.; Traverso, A.; Wee, L.; van Kuijk, S.M.J. Prediction modeling methodology. In: Fundamentals of Clinical Data Science; Kubben, P.; Dumontier, M.; Dekker, A., Eds.; Springer: Cham, CH, 2019.
[http://dx.doi.org/10.1007/978-3-319-99713-1_8]
[313]
Brown, J.B. Classifiers and their metrics quantified. Mol. Inform., 2018, 37(1-2), 1700127.
[http://dx.doi.org/10.1002/minf.201700127] [PMID: 29360259]
[314]
Chicco, D.; Jurman, G. The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation. BMC Genom., 2020, 21(1), 6.
[http://dx.doi.org/10.1186/s12864-019-6413-7] [PMID: 31898477]
[315]
Chicco, D.; Tötsch, N.; Jurman, G. The Matthews correlation coefficient (MCC) is more reliable than balanced accuracy, bookmaker informedness, and markedness in two-class confusion matrix evaluation. BioData Min., 2021, 14(1), 13.
[http://dx.doi.org/10.1186/s13040-021-00244-z] [PMID: 33541410]
[316]
Delacour, H.; Servonnet, A.; Perrot, A.; Vigezzi, J.F.; Ramirez, J.M. ROC (receiver operating characteristics) curve: Principles and application in biology. Ann. Biol. Clin. (Paris), 2005, 63(2), 145-154.
[PMID: 15771972]
[317]
Munir, K.; Elahi, H.; Ayub, A.; Frezza, F.; Rizzi, A. Cancer diagnosis using deep learning: A bibliographic review. Cancers (Basel), 2019, 11(9), 1235.
[http://dx.doi.org/10.3390/cancers11091235] [PMID: 31450799]
[318]
Delgado, R.; Tibau, X.A. Why Cohen’s kappa should be avoided as performance measure in classification. PLoS One, 2019, 14(9), e0222916.
[http://dx.doi.org/10.1371/journal.pone.0222916] [PMID: 31557204]
[319]
Gunst, R.F.; Mason, R.L. Biased estimation in regression: An evaluation using mean squared error. J. Am. Stat. Assoc., 1977, 72(359), 616-628.
[http://dx.doi.org/10.1080/01621459.1977.10480625]
[320]
Linnet, K. Evaluation of regression procedures for methods comparison studies. Clin. Chem., 1993, 39(3), 424-432.
[http://dx.doi.org/10.1093/clinchem/39.3.424] [PMID: 8448852]
[321]
de Myttenaere, A.; Golden, B.; Le Grand, B.; Rossi, F. Mean absolute percentage error for regression models. Neurocomputing, 2016, 192, 38-48.
[http://dx.doi.org/10.1016/j.neucom.2015.12.114]
[322]
Helland, I.S. On the interpretation and use of R2 in regression analysis. Biometrics, 1987, 43(1), 61-69.
[http://dx.doi.org/10.2307/2531949]
[323]
Ballester, P.J. Machine learning for molecular modelling in drug design. Biomolecules, 2019, 9(6), 216.
[http://dx.doi.org/10.3390/biom9060216] [PMID: 31167503]
[324]
Sawada, R.; Kotera, M.; Yamanishi, Y. Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach. Mol. Inform., 2014, 33(11-12), 719-731.
[http://dx.doi.org/10.1002/minf.201400066] [PMID: 27485418]
[325]
Wójcikowski, M.; Siedlecki, P.; Ballester, P.J. Building machine-learning scoring functions for structure-based prediction of intermolecular binding affinity. Methods Mol. Biol., 2019, 2053, 1-12.
[http://dx.doi.org/10.1007/978-1-4939-9752-7_1] [PMID: 31452095]
[326]
Li, H.; Leung, K.S.; Wong, M.H.; Ballester, P.J. Improving autodock vina using random forest: The growing accuracy of binding affinity prediction by the effective exploitation of larger data sets. Mol. Inform., 2015, 34(2-3), 115-126.
[http://dx.doi.org/10.1002/minf.201400132] [PMID: 27490034]
[327]
Wójcikowski, M.; Ballester, P.J.; Siedlecki, P. Performance of machine-learning scoring functions in structure-based virtual screening. Sci. Rep., 2017, 7(1), 46710.
[http://dx.doi.org/10.1038/srep46710] [PMID: 28440302]
[328]
Fresnais, L.; Ballester, P.J. The impact of compound library size on the performance of scoring functions for structure-based virtual screening. Brief. Bioinform., 2021, 22, bbaa095.
[http://dx.doi.org/10.1093/bib/bbaa095]
[329]
Pereira, J.C.; Caffarena, E.R.; dos Santos, C.N. Boosting docking-based virtual screening with deep learning. J. Chem. Inf. Model., 2016, 56(12), 2495-2506.
[http://dx.doi.org/10.1021/acs.jcim.6b00355] [PMID: 28024405]
[330]
ECHA. Practical Guide 5: How to Use and Report (Q); SARS, 2016.
[331]
Vilar, S.; Costanzi, S. Predicting the biological activities through QSAR analysis and docking-based scoring. Methods Mol. Biol., 2012, 914, 271-284.
[http://dx.doi.org/10.1007/978-1-62703-023-6_16] [PMID: 22976034]
[332]
Kausar, S.; Falcao, A.O. An automated framework for QSAR model building. J. Cheminform., 2018, 10(1), 1.
[http://dx.doi.org/10.1186/s13321-017-0256-5] [PMID: 29340790]
[333]
Tsou, L.K.; Yeh, S.H.; Ueng, S.H.; Chang, C.P.; Song, J.S.; Wu, M.H.; Chang, H.F.; Chen, S.R.; Shih, C.; Chen, C.T.; Ke, Y.Y. Comparative study between deep learning and QSAR classifications for TNBC inhibitors and novel GPCR agonist discovery. Sci. Rep., 2020, 10(1), 16771.
[http://dx.doi.org/10.1038/s41598-020-73681-1] [PMID: 33033310]
[334]
Myint, K.Z.; Xie, X.Q. Recent advances in fragment-based QSAR and multi-dimensional QSAR methods. Int. J. Mol. Sci., 2010, 11(10), 3846-3866.
[http://dx.doi.org/10.3390/ijms11103846] [PMID: 21152304]
[335]
Martin, E.; Mukherjee, P.; Sullivan, D.; Jansen, J. Profile-QSAR: A novel meta-QSAR method that combines activities across the kinase family to accurately predict affinity, selectivity, and cellular activity. J. Chem. Inf. Model., 2011, 51(8), 1942-1956.
[http://dx.doi.org/10.1021/ci1005004] [PMID: 21667971]
[336]
Zhong, M.; Xuan, S.; Wang, L.; Hou, X.; Wang, M.; Yan, A.; Dai, B. Prediction of bioactivity of ACAT2 inhibitors by multilinear regression analysis and support vector machine. Bioorg. Med. Chem. Lett., 2013, 23(13), 3788-3792.
[http://dx.doi.org/10.1016/j.bmcl.2013.04.087] [PMID: 23711921]
[337]
Daynac, M.; Cortes-Cabrera, A.; Prieto, J.M. Application of artificial intelligence to the prediction of the antimicrobial activity of essential oils. Evid. Based Complement. Alternat. Med., 2015, 2015, 1-9.
[http://dx.doi.org/10.1155/2015/561024] [PMID: 26457111]
[338]
Kumari, M.; Chandra, S. In silico prediction of anti-malarial hit molecules based on machine learning methods. Int. J. Comput. Biol. Drug Des., 2015, 8(1), 40-53.
[http://dx.doi.org/10.1504/IJCBDD.2015.068783] [PMID: 25869318]
[339]
Malik, A.A.; Phanus-umporn, C.; Schaduangrat, N.; Shoombuatong, W.; Isarankura-Na-Ayudhya, C.; Nantasenamat, C. HCVPRED: A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors. J. Comput. Chem., 2020, 41(20), 1820-1834.
[http://dx.doi.org/10.1002/jcc.26223] [PMID: 32449536]
[340]
Tripathi, N.; Goshisht, M.K.; Sahu, S.K.; Arora, C. Applications of artificial intelligence to drug design and discovery in the big data era: A comprehensive review. Mol. Divers., 2021, 25(3), 1643-1664.
[http://dx.doi.org/10.1007/s11030-021-10237-z] [PMID: 34110579]
[341]
Dahl, G.E.; Jaitly, N.; Salakhutdinov, R. Multi-task neural networks for QSAR predictions. ArXiv, 2014, 2014, 14061231.
[342]
Ponzoni, I.; Sebastián-Pérez, V.; Requena-Triguero, C.; Roca, C.; Martínez, M.J.; Cravero, F.; Díaz, M.F.; Páez, J.A.; Arrayás, R.G.; Adrio, J.; Campillo, N.E. Hybridizing feature selection and feature learning approaches in QSAR modeling for drug discovery. Sci. Rep., 2017, 7(1), 2403.
[http://dx.doi.org/10.1038/s41598-017-02114-3] [PMID: 28546583]
[343]
Ramsundar, B.; Liu, B.; Wu, Z.; Verras, A.; Tudor, M.; Sheridan, R.P.; Pande, V. Is multitask deep learning practical for pharma? J. Chem. Inf. Model., 2017, 57(8), 2068-2076.
[http://dx.doi.org/10.1021/acs.jcim.7b00146] [PMID: 28692267]
[344]
Markoff, J. Scientists see promise in deep-learning programs, nytimes. Httpnyti MssgcVec 2012. Available from: http://web. mit.edu/course/other/i2course/www/deep/ssee.pdf
[345]
Vamathevan, J.; Clark, D.; Czodrowski, P.; Dunham, I.; Ferran, E.; Lee, G.; Li, B.; Madabhushi, A.; Shah, P.; Spitzer, M.; Zhao, S. Applications of machine learning in drug discovery and development. Nat. Rev. Drug Discov., 2019, 18(6), 463-477.
[http://dx.doi.org/10.1038/s41573-019-0024-5] [PMID: 30976107]
[346]
(a)Abadi, M.; Agarwal, A.; Barham, P.; Brevdo, E.; Chen, Z.; Citro, C.; Corrado, G.S.; Davis, A.; Dean, J.; Devin, M. Tensorflow: Large-scale machine learning on heterogeneous systems. Tensorflow. Org; , 2016. Available from: https://Www. Tensorflow. Org/
(b)Cybenko, George Approximation by superpositions of a sigmoidal function. Math. Control Signals Syst., 1989, 2, 303-314.
[347]
Paszke, A.; Gross, S.; Massa, F.; Lerer, A.; Bradbury, J.; Chanan, G.; Killeen, T.; Lin, Z.; Gimelshein, N.; Antiga, L. Pytorch: An imperative style, high-performance deep learning library. Adv. Neural Inf. Process. Syst., 2019, 32.
[348]
Pedregosa, F.; Varoquaux, G.; Gramfort, A.; Michel, V.; Thirion, B.; Grisel, O.; Blondel, M.; Prettenhofer, P.; Weiss, R.; Dubourg, V. Scikit-learn: Machine learning in python. J. Mach. Learn. Res., 2011, 12, 2825-2830.
[349]
Chollet, F.K. Available from:. Https://Keras. Io (Accessed on 14 August 2019).
[350]
Yu, T-H.; Su, B-H.; Battalora, L.C.; Liu, S.; Tseng, Y.J. Ensemble modeling with machine learning and deep learning to provide interpretable generalized rules for classifying CNS drugs with high prediction power. Brief. Bioinform., 2022, 23, bbab377.
[http://dx.doi.org/10.1093/bib/bbab377]
[351]
Gentile, F.; Agrawal, V.; Hsing, M.; Ton, A.T.; Ban, F.; Norinder, U.; Gleave, M.E.; Cherkasov, A. Deep docking: A deep learning platform for augmentation of structure based drug discovery. ACS Cent. Sci., 2020, 6(6), 939-949.
[http://dx.doi.org/10.1021/acscentsci.0c00229] [PMID: 32607441]
[352]
Playe, B.; Stoven, V. Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity. J. Cheminform., 2020, 12(1), 11.
[http://dx.doi.org/10.1186/s13321-020-0413-0] [PMID: 33431042]
[353]
Asmare, M.M.; Nitin, N.; Yun, S.I.L.; Mahapatra, R.K. QSAR and deep learning model for virtual screening of potential inhibitors against Inosine 5′ Monophosphate dehydrogenase (IMPDH) of Cryptosporidium parvum. J. Mol. Graph. Model., 2022, 111, 108108.
[http://dx.doi.org/10.1016/j.jmgm.2021.108108] [PMID: 34911011]
[354]
Li, Y.; Xu, Y.; Yu, Y. CRNNTL: Convolutional Recurrent Neural Network and Transfer Learning for QSAR modeling in organic drug and material discovery. Molecules, 2021, 26(23), 7257.
[http://dx.doi.org/10.3390/molecules26237257] [PMID: 34885843]
[355]
Jumper, J.; Evans, R.; Pritzel, A.; Green, T.; Figurnov, M.; Ronneberger, O.; Tunyasuvunakool, K.; Bates, R.; Žídek, A.; Potapenko, A.; Bridgland, A.; Meyer, C.; Kohl, S.A.A.; Ballard, A.J.; Cowie, A.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Adler, J.; Back, T.; Petersen, S.; Reiman, D.; Clancy, E.; Zielinski, M.; Steinegger, M.; Pacholska, M.; Berghammer, T.; Bodenstein, S.; Silver, D.; Vinyals, O.; Senior, A.W.; Kavukcuoglu, K.; Kohli, P.; Hassabis, D. Highly accurate protein structure prediction with AlphaFold. Nature, 2021, 596(7873), 583-589.
[http://dx.doi.org/10.1038/s41586-021-03819-2] [PMID: 34265844]
[356]
Baek, M.; DiMaio, F.; Anishchenko, I.; Dauparas, J.; Ovchinnikov, S.; Lee, G.R.; Wang, J.; Cong, Q.; Kinch, L.N.; Schaeffer, R.D.; Millán, C.; Park, H.; Adams, C.; Glassman, C.R.; DeGiovanni, A.; Pereira, J.H.; Rodrigues, A.V.; van Dijk, A.A.; Ebrecht, A.C.; Opperman, D.J.; Sagmeister, T.; Buhlheller, C.; Pavkov-Keller, T.; Rathinaswamy, M.K.; Dalwadi, U.; Yip, C.K.; Burke, J.E.; Garcia, K.C.; Grishin, N.V.; Adams, P.D.; Read, R.J.; Baker, D. Accurate prediction of protein structures and interactions using a three-track neural network. Science, 2021, 373(6557), 871-876.
[http://dx.doi.org/10.1126/science.abj8754] [PMID: 34282049]
[357]
Zheng, W.; Li, Y.; Zhang, C.; Zhou, X.; Pearce, R.; Bell, E.W.; Huang, X.; Zhang, Y. Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14. Proteins, 2021, 89(12), 1734-1751.
[http://dx.doi.org/10.1002/prot.26193] [PMID: 34331351]
[358]
Torrisi, M.; Pollastri, G.; Le, Q. Deep learning methods in protein structure prediction. Comput. Struct. Biotechnol. J., 2020, 18, 1301-1310.
[http://dx.doi.org/10.1016/j.csbj.2019.12.011] [PMID: 32612753]
[359]
Lyu, Z.; Wang, Z.; Luo, F.; Shuai, J.; Huang, Y. Protein secondary structure prediction with a reductive deep learning method. Front. Bioeng. Biotechnol., 2021, 9, 687426.
[http://dx.doi.org/10.3389/fbioe.2021.687426] [PMID: 34211967]
[360]
Anishchenko, I.; Baek, M.; Park, H.; Hiranuma, N.; Kim, D.E.; Dauparas, J.; Mansoor, S.; Humphreys, I.R.; Baker, D. Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14. Proteins, 2021, 89(12), 1722-1733.
[http://dx.doi.org/10.1002/prot.26194] [PMID: 34331359]
[361]
Mulnaes, D.; Koenig, F.; Gohlke, H. TopSuite Web Server: A meta-suite for deep-learning-based protein structure and quality prediction. J. Chem. Inf. Model., 2021, 61(2), 548-553.
[http://dx.doi.org/10.1021/acs.jcim.0c01202] [PMID: 33464891]
[362]
Sadek, A.; Zaha, D.; Ahmed, M.S. Structural insights of SARS-CoV-2 spike protein from delta and omicron variants. bioRxiv, 2021, 2021., 2021.12.08.471777.
[http://dx.doi.org/10.1101/2021.12.08.471777]
[363]
Stokes, J.M.; Yang, K.; Swanson, K.; Jin, W.; Cubillos-Ruiz, A.; Donghia, N.M.; MacNair, C.R.; French, S.; Carfrae, L.A.; Bloom-Ackermann, Z.; Tran, V.M.; Chiappino-Pepe, A.; Badran, A.H.; Andrews, I.W.; Chory, E.J.; Church, G.M.; Brown, E.D.; Jaakkola, T.S.; Barzilay, R.; Collins, J.J. A deep learning approach to antibiotic discovery. Cell, 2020, 180(4), 688-702.e13.
[http://dx.doi.org/10.1016/j.cell.2020.01.021] [PMID: 32084340]
[364]
Neves, B.J.; Braga, R.C.; Alves, V.M.; Lima, M.N.N.; Cassiano, G.C.; Muratov, E.N.; Costa, F.T.M.; Andrade, C.H. Deep learning-driven research for drug discovery: Tackling malaria. PLOS Comput. Biol., 2020, 16(2), e1007025.
[http://dx.doi.org/10.1371/journal.pcbi.1007025] [PMID: 32069285]
[365]
Pan, C.; Schoppe, O.; Parra-Damas, A.; Cai, R.; Todorov, M.I.; Gondi, G.; von Neubeck, B.; Böğürcü-Seidel, N.; Seidel, S.; Sleiman, K.; Veltkamp, C.; Förstera, B.; Mai, H.; Rong, Z.; Trompak, O.; Ghasemigharagoz, A.; Reimer, M.A.; Cuesta, A.M.; Coronel, J.; Jeremias, I.; Saur, D.; Acker-Palmer, A.; Acker, T.; Garvalov, B.K.; Menze, B.; Zeidler, R.; Ertürk, A. Deep learning reveals cancer metastasis and therapeutic antibody targeting in the entire body. Cell, 2019, 179(7), 1661-1676.e19.
[http://dx.doi.org/10.1016/j.cell.2019.11.013] [PMID: 31835038]
[366]
Zhu, W.; Xie, L.; Han, J.; Guo, X. The application of deep learning in cancer prognosis prediction. Cancers (Basel), 2020, 12(3), 603.
[http://dx.doi.org/10.3390/cancers12030603] [PMID: 32150991]
[367]
Tran, K.A.; Kondrashova, O.; Bradley, A.; Williams, E.D.; Pearson, J.V.; Waddell, N. Deep learning in cancer diagnosis, prognosis and treatment selection. Genome Med., 2021, 13(1), 152.
[http://dx.doi.org/10.1186/s13073-021-00968-x] [PMID: 34579788]
[368]
Kuenzi, B.M.; Park, J.; Fong, S.H.; Sanchez, K.S.; Lee, J.; Kreisberg, J.F.; Ma, J.; Ideker, T. Predicting drug response and synergy using a deep learning model of human cancer cells. Cancer Cell, 2020, 38(5), 672-684.e6.
[http://dx.doi.org/10.1016/j.ccell.2020.09.014] [PMID: 33096023]
[369]
Zuo, Z.; Wang, P.; Chen, X.; Tian, L.; Ge, H.; Qian, D. SWnet: A deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures. BMC Bioinform., 2021, 22(1), 434.
[http://dx.doi.org/10.1186/s12859-021-04352-9] [PMID: 34507532]
[370]
Wang, Y.W.; Huang, L.; Jiang, S.W.; Li, K.; Zou, J.; Yang, S.Y. CapsCarcino: A novel sparse data deep learning tool for predicting carcinogens. Food Chem. Toxicol., 2020, 135, 110921.
[http://dx.doi.org/10.1016/j.fct.2019.110921] [PMID: 31669597]
[371]
Kusumoto, D.; Seki, T.; Sawada, H.; Kunitomi, A.; Katsuki, T.; Kimura, M.; Ito, S.; Komuro, J.; Hashimoto, H.; Fukuda, K.; Yuasa, S. Anti-senescent drug screening by deep learning-based morphology senescence scoring. Nat. Commun., 2021, 12(1), 257.
[http://dx.doi.org/10.1038/s41467-020-20213-0] [PMID: 33431893]
[372]
Jin, W.; Stokes, J.M.; Eastman, R.T.; Itkin, Z.; Zakharov, A.V.; Collins, J.J.; Jaakkola, T.S.; Barzilay, R. Deep learning identifies synergistic drug combinations for treating COVID-19. Proc. Natl. Acad. Sci. USA, 2021, 118(39), e2105070118.
[http://dx.doi.org/10.1073/pnas.2105070118] [PMID: 34526388]
[373]
Desai, S.B.; Pareek, A.; Lungren, M.P. Deep learning and its role in COVID-19 medical imaging. Intell.-. Based Med., 2020, 3-4, 100013.
[http://dx.doi.org/10.1016/j.ibmed.2020.100013] [PMID: 33169117]
[374]
Timmons, P.B.; Hewage, C.M. ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides. Brief. Bioinform., 2021, 22, bbab258.
[http://dx.doi.org/10.1093/bib/bbab258]
[375]
Andrianov, A.M.; Nikolaev, G.I.; Shuldov, N.A.; Bosko, I.P.; Anischenko, A.I.; Tuzikov, A.V. Application of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors. J. Biomol. Struct. Dyn., 2021, 1-19.
[http://dx.doi.org/10.1080/07391102.2021.1905559] [PMID: 33855929]
[376]
Li, J.; Pu, Y.; Tang, J.; Zou, Q.; Guo, F. DeepAVP: A dual-channel deep neural network for identifying variable-length antiviral peptides. IEEE J. Biomed. Health Inform., 2020, 24(10), 3012-3019.
[http://dx.doi.org/10.1109/JBHI.2020.2977091] [PMID: 32142462]
[377]
Pan, X.; Zuallaert, J.; Wang, X.; Shen, H.B.; Campos, E.P.; Marushchak, D.O.; De Neve, W.; Tox, D.L. ToxDL Deep learning using primary structure and domain embeddings for assessing protein toxicity. Bioinformatics, 2021, 36(21), 5159-5168.
[http://dx.doi.org/10.1093/bioinformatics/btaa656] [PMID: 32692832]
[378]
Zhang, J.; Norinder, U.; Svensson, F. Deep learning-based conformal prediction of toxicity. J. Chem. Inf. Model., 2021, 61(6), 2648-2657.
[http://dx.doi.org/10.1021/acs.jcim.1c00208] [PMID: 34043352]
[379]
Karim, A.; Riahi, V.; Mishra, A.; Newton, M.A.H.; Dehzangi, A.; Balle, T.; Sattar, A. Quantitative toxicity prediction via meta ensembling of multitask deep learning models. ACS Omega, 2021, 6(18), 12306-12317.
[http://dx.doi.org/10.1021/acsomega.1c01247] [PMID: 34056383]
[380]
Wei, L.; Ye, X.; Sakurai, T.; Mu, Z.; Wei, L. ToxIBTL: Prediction of peptide toxicity based on information bottleneck and transfer learning. Bioinforma. Oxf. Engl., 2022, 2022, btac006.
[381]
Wang, D.; Liu, W.; Shen, Z.; Jiang, L.; Wang, J.; Li, S.; Li, H. Deep learning based drug metabolites prediction. Front. Pharmacol., 2020, 10, 1586.
[http://dx.doi.org/10.3389/fphar.2019.01586] [PMID: 32082146]
[382]
Yan, J.; Bhadra, P.; Li, A.; Sethiya, P.; Qin, L.; Tai, H.K.; Wong, K.H.; Siu, S.W.I. Deep-AmPEP30: Improve short antimicrobial peptides prediction with deep learning. Mol. Ther. Nucleic Acids, 2020, 20, 882-894.
[http://dx.doi.org/10.1016/j.omtn.2020.05.006] [PMID: 32464552]
[383]
Peng, Y.; Zhang, Z.; Jiang, Q.; Guan, J.; Zhou, S. TOP: A deep mixture representation learning method for boosting molecular toxicity prediction. Methods, 2020, 179, 55-64.
[http://dx.doi.org/10.1016/j.ymeth.2020.05.013] [PMID: 32446957]
[384]
Jimenez-Carretero, D.; Abrishami, V.; Fernández-de-Manuel, L.; Palacios, I.; Quílez-Álvarez, A.; Díez-Sánchez, A.; del Pozo, M.A.; Montoya, M.C. Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening. PLOS Comput. Biol., 2018, 14(11), e1006238.
[http://dx.doi.org/10.1371/journal.pcbi.1006238] [PMID: 30500821]
[385]
Li, T.; Tong, W.; Roberts, R.; Liu, Z.; Thakkar, S. Deep learning on high-throughput transcriptomics to predict drug-induced liver injury. Front. Bioeng. Biotechnol., 2020, 8, 562677.
[http://dx.doi.org/10.3389/fbioe.2020.562677] [PMID: 33330410]
[386]
Wan, F.; Zhu, Y.; Hu, H.; Dai, A.; Cai, X.; Chen, L.; Gong, H.; Xia, T.; Yang, D.; Wang, M.W.; Zeng, J. DeepCPI: A deep learning-based framework for large-scale in silico drug screening. Genom. Proteom. Bioinform., 2019, 17(5), 478-495.
[http://dx.doi.org/10.1016/j.gpb.2019.04.003] [PMID: 32035227]
[387]
Wen, M.; Zhang, Z.; Niu, S.; Sha, H.; Yang, R.; Yun, Y.; Lu, H. Deep-learning-based drug–target interaction prediction. J. Proteome Res., 2017, 16(4), 1401-1409.
[http://dx.doi.org/10.1021/acs.jproteome.6b00618] [PMID: 28264154]
[388]
Zhao, Y.; Zheng, K.; Guan, B.; Guo, M.; Song, L.; Gao, J.; Qu, H.; Wang, Y.; Shi, D.; Zhang, Y. DLDTI: A learning-based framework for drug-target interaction identification using neural networks and network representation. J. Transl. Med., 2020, 18(1), 434.
[http://dx.doi.org/10.1186/s12967-020-02602-7] [PMID: 33187537]
[389]
Xie, L.; He, S.; Song, X.; Bo, X.; Zhang, Z. Deep learning-based transcriptome data classification for drug-target interaction prediction. BMC Genomics, 2018, 19(Suppl. 7), 667.
[http://dx.doi.org/10.1186/s12864-018-5031-0] [PMID: 30255785]
[390]
Zhao, T.; Hu, Y.; Valsdottir, L.R.; Zang, T.; Peng, J. Identifying drug–target interactions based on graph convolutional network and deep neural network. Brief. Bioinform., 2021, 22(2), 2141-2150.
[http://dx.doi.org/10.1093/bib/bbaa044] [PMID: 32367110]
[391]
Salmon, J.W.; Thompson, S.L. Big data: information technology as control over the profession of medicine. In: The Corporatization of American Health Care; Springer, 2021; pp. 181-254.
[http://dx.doi.org/10.1007/978-3-030-60667-1_5]
[392]
Tung, J. Pfizer and IBM: A collaboration to accelerate drug discovery?. Technology and Operations Management. Available from: https://digital.hbs.edu/platform-rctom/submission/pfizer-and-ibm-a-collaboration-to-accelerate-drug-discovery/ (accessed 2022-08-01).
[393]
Freedman, D.H. Hunting for new drugs with AI. Nature, 2019, 576(7787), S49-S53.
[http://dx.doi.org/10.1038/d41586-019-03846-0] [PMID: 31853074]
[394]
Savage, N. Tapping into the drug discovery potential of AI. Biopharma Deal, 2021. Available form: https://www.nature.com/articles/d43747-021-00045-7
[http://dx.doi.org/10.1038/d43747-021-00045-7]
[395]
Probst, C.; Schneider, S.; Loskill, P. High-throughput organ-on-a-chip systems: Current status and remaining challenges. Curr. Opin. Biomed. Eng., 2018, 6, 33-41.
[http://dx.doi.org/10.1016/j.cobme.2018.02.004]
[396]
Vatansever, S.; Schlessinger, A.; Wacker, D.; Kaniskan, H.Ü.; Jin, J.; Zhou, M.M.; Zhang, B. Artificial intelligence and machine learning‐aided drug discovery in central nervous system diseases: State‐of‐the‐arts and future directions. Med. Res. Rev., 2021, 41(3), 1427-1473.
[http://dx.doi.org/10.1002/med.21764] [PMID: 33295676]
[397]
Choi, R.Y.; Coyner, A.S.; Kalpathy-Cramer, J.; Chiang, M.F.; Campbell, J.P. Introduction to machine learning, neural networks, and deep learning. Transl. Vis. Sci. Technol., 2020, 9(2), 14.
[PMID: 32704420]
[398]
Gundersen, S.; Boddu, S.; Capella-Gutierrez, S.; Drabløs, F.; Fernández, J.M.; Kompova, R.; Taylor, K.; Titov, D.; Zerbino, D.; Hovig, E. Recommendations for the FAIRification of genomic track metadata. F1000 Res., 2021, 10, 268.
[http://dx.doi.org/10.12688/f1000research.28449.1] [PMID: 34249331]
[399]
Gabernet, A.R.; Limburn, J. Breaking the 80/20 Rule: How data catalogs transform data scientists’ productivity. IBM Cloud Blog; Available from, 2017. https://www.ibm.com/cloud/blog/ibm-data-catalog-data-scientists-productivity
[400]
Boniolo, F.; Dorigatti, E.; Ohnmacht, A.J.; Saur, D.; Schubert, B.; Menden, M.P. Artificial intelligence in early drug discovery enabling precision medicine. Expert Opin. Drug Discov., 2021, 16(9), 991-1007.
[http://dx.doi.org/10.1080/17460441.2021.1918096] [PMID: 34075855]
[401]
Ghassemi, M.; Oakden-Rayner, L.; Beam, A.L. The false hope of current approaches to explainable artificial intelligence in health care. Lancet Digit. Health, 2021, 3(11), e745-e750.
[http://dx.doi.org/10.1016/S2589-7500(21)00208-9] [PMID: 34711379]
[402]
Paul, D.; Sanap, G.; Shenoy, S.; Kalyane, D.; Kalia, K.; Tekade, R.K. Artificial intelligence in drug discovery and development. Drug Discov. Today, 2021, 26(1), 80-93.
[http://dx.doi.org/10.1016/j.drudis.2020.10.010] [PMID: 33099022]
[403]
Stone, J.E.; Hardy, D.J.; Ufimtsev, I.S.; Schulten, K. GPU-accelerated molecular modeling coming of age. J. Mol. Graph. Model., 2010, 29(2), 116-125.
[http://dx.doi.org/10.1016/j.jmgm.2010.06.010] [PMID: 20675161]

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