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


Abdallah Sayyed-Ahmad*   Pages 1 - 6 ( 6 )


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 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.


binding site identification, co-solvents, fragment-based, probe-based, hotspots, structure-based drug design


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

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