Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach.

ABSTRACT: The site identification by ligand competitive saturation (SILCS) method identifies the location and approximate affinities of small molecular fragments on a target macromolecular surface by performing molecular dynamics (MD) simulations of the target in an aqueous solution of small molecules representative of different chemical functional groups. In this study, we introduce a set of small molecules to map potential interactions made by neutral hydrogen bond donors and acceptors and charged donor and acceptor fragments in addition to nonpolar fragments. The affinity pattern is obtained in the form of discretized probability or, equivalently, free energy maps, called FragMaps, which can be visualized with the target surface. We performed SILCS simulations for four proteins for which structur

SUBMITTER: Raman EP 

PROVIDER: S-EPMC3947602 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature