Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.

ABSTRACT: Site Identification by Ligand Competitive Saturation (SILCS) is a molecular simulation approach that uses diverse small solutes in aqueous solution to obtain functional group affinity patterns of a protein or other macromolecule. This involves employing a combined Grand Canonical Monte Carlo (GCMC)-molecular dynamics (MD) method to sample the full 3D space of the protein, including deep binding pockets and interior cavities from which functional group free energy maps (FragMaps) are obtained. The information content in the maps, which include contributions from protein flexibilty and both protein and functional group desolvation contributions, can be used in many aspects of the drug discovery process. These include identification of novel ligand binding pockets, including allosteric sites,

SUBMITTER: Goel H 

PROVIDER: S-EPMC8863107 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature