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Current Topics in Medicinal Chemistry

Editor-in-Chief

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

Review Article

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

Author(s): Abdallah Sayyed-Ahmad*

Volume 18, Issue 27, 2018

Page: [2278 - 2283] Pages: 6

DOI: 10.2174/1568026619666181130120308

Price: $65

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.

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


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