title: Emerging methods for ensemble-based virtual screening.
abstract: Ensemble based virtual screening refers to the use of conformational ensembles from crystal structures, NMR studies or molecular dynamics simulations. It has gained greater acceptance as advances in the theoretical framework, computational algorithms, and software packages enable simulations at longer time scales. Here we focus on the use of computationally generated conformational ensembles and emerging methods that use these ensembles for discovery, such as the Relaxed Complex Scheme or Dynamic Pharmacophore Model. We also discuss the more rigorous physics-based computational techniques such as accelerated molecular dynamics and thermodynamic integration and their applications in improving conformational sampling or the ranking of virtual screening hits. Finally, technological advances that will help make virtual screening tools more accessible to a wider audience in computer aided drug design are discussed.
authors.affiliation: Department of Pharmaceutical Sciences and Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. ramaro@uci.edu
authors.forename: Rommie E
authors.initials: RE
authors.lastname: Amaro
authors.forename: Wilfred W
authors.initials: WW
authors.lastname: Li
mesh_terms: D000465:Algorithms; D017076:Computer-Aided Design; D015195:Drug Design; D055808:Drug Discovery; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D013678:Technology, Pharmaceutical / Q000379:methods*
chemical_list: D004364:Pharmaceutical Preparations