title: Docking: successes and challenges.
abstract: The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fundamental issues and challenges involved in comparing various docking methods are discussed. Limitations of current technologies as well as future prospects are presented.
authors.affiliation: 3-Dimensional Pharmaceuticals, Cedarbrook Corporate Center, 8 Clarke Drive, Cranbury, NJ 08512, USA. vmohan@prdus.jnj.com
authors.forename: Venkatraman
authors.initials: V
authors.lastname: Mohan
authors.forename: Alan C
authors.initials: AC
authors.lastname: Gibbs
authors.forename: Maxwell D
authors.initials: MD
authors.lastname: Cummings
authors.forename: Edward P
authors.initials: EP
authors.lastname: Jaeger
authors.forename: Renee L
authors.initials: RL
authors.lastname: DesJarlais
mesh_terms: D000465:Algorithms; D017076:Computer-Aided Design / Q000639:trends; D016503:Drug Delivery Systems / Q000379:methods; D008024:Ligands; D008565:Membrane Proteins; D011485:Protein Binding; D013678:Technology, Pharmaceutical / Q000379:methods* / Q000639:trends*
chemical_list: D008024:Ligands; D008565:Membrane Proteins; C035026:SRPRA protein, human