Overview of Free Software Developed for Designing Drugs Based on Protein-Small Molecules Interaction

Title:Overview of Free Software Developed for Designing Drugs Based on Protein-Small Molecules Interaction

Volume: 18 Issue: 13

Author(s): Piyush Agrawal, Pawan Kumar Raghav, Sherry Bhalla, Neelam Sharma and Gajendra P.S. Raghava*

Affiliation:

• Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi,India

Keywords: Protein-small molecule interaction, Structure Prediction, Docking, Pharmacophore, Molecular Dynamics, Post Translational Modifications.

Abstract: One of the fundamental challenges in designing drug molecule against a disease target or protein is to predict binding affinity between target and drug or small molecule. In this review, our focus will be on advancement in the field of protein-small molecule interaction. This review has been divided into four major sections. In the first section, we will cover software developed for protein structure prediction. This will include prediction of binding pockets and post-translation modifications in proteins. In the second section, we will discuss software packages developed for predicting small-molecule interacting residues in a protein. Advances in the field of docking particularly advancement in the knowledgebased force fields will be discussed in the third part of the review. This section will also cover the method developed for predicting affinity between protein and drug molecules. The fourth section of the review will describe miscellaneous techniques used for designing drug molecules, like pharmacophore modelling. Our major emphasis in this review will be on computational tools that are available free for academic use.

Cite this article as:

Agrawal Piyush , Raghav Kumar Pawan , Bhalla Sherry , Sharma Neelam and Raghava P.S. Gajendra *, Overview of Free Software Developed for Designing Drugs Based on Protein-Small Molecules Interaction, Current Topics in Medicinal Chemistry 2018; 18 (13) . https://dx.doi.org/10.2174/1568026618666180816155131