title: On the use of molecular dynamics receptor conformations for virtual screening.
abstract: Receptors are inherently dynamic and this flexibility is important to consider when constructing a model of molecular association. Conformations from molecular dynamics simulations, a well-established method for examining protein dynamics, can be used in virtual screening to account for flexibility in structure-based drug discovery. Different receptor configurations influence docking results. Molecular dynamics simulations can provide snapshots that improve virtual screening predictive power over known crystal structures, most likely as a result of sampling more relevant receptor conformations. Here we highlight some details and nuances of using such snapshots and evaluating them for predictive performance.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA. senichols@ucsd.edu
authors.forename: Sara E
authors.initials: SE
authors.lastname: Nichols
authors.forename: Riccardo
authors.initials: R
authors.lastname: Baron
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D018360:Crystallography, X-Ray; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011956:Receptors, Cell Surface / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D011956:Receptors, Cell Surface