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

[ Vol. 18 , Issue. 27 ]

Author(s):

Abdallah Sayyed-Ahmad*   Pages 2278 - 2283 ( 6 )

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.

Affiliation:

Department of Physics, Birzeit University, PO BOX 14, Birzeit



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