Hotspot Identification on Protein Surfaces Using Probe-Based MD Simulations: Successes and Challenges

Title:Hotspot Identification on Protein Surfaces Using Probe-Based MD Simulations: Successes and Challenges

Volume: 18 Issue: 27

Author(s): Abdallah Sayyed-Ahmad*

Affiliation:

• Department of Physics, Birzeit University, PO BOX 14, Birzeit,Palestinian Territory, Occupied

Keywords: Binding site identification, Co-solvents, fragment-based, Probe-based, Hotspots, Structure-based drug design.

Abstract: Molecular Dynamics (MD) based computational co-solvent mapping methods involve the generation of an ensemble of MD-sampled target protein conformations and using selected small molecule fragments to identify and characterize binding sites on the surface of a target protein. This approach incorporates atomic-level solvation effects and protein mobility. It has shown great promise in the identification of conventional competitive and allosteric binding sites. It is also currently emerging as a useful tool in the early stages of drug discovery. This review summarizes efforts as well as discusses some methodological advances and challenges in binding site identification process through these co-solvent mapping methods.

Cite this article as:

Sayyed-Ahmad Abdallah *, Hotspot Identification on Protein Surfaces Using Probe-Based MD Simulations: Successes and Challenges, Current Topics in Medicinal Chemistry 2018; 18 (27) . https://dx.doi.org/10.2174/1568026619666181130120308