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
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.
