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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