Docking: successes and challenges.
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.
Mohan
Venkatraman
V
3-Dimensional Pharmaceuticals, Cedarbrook Corporate Center, 8 Clarke Drive, Cranbury, NJ 08512, USA. vmohan@prdus.jnj.com
Gibbs
Alan C
AC
Cummings
Maxwell D
MD
Jaeger
Edward P
EP
DesJarlais
Renee L
RL
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*
D008024:Ligands; D008565:Membrane Proteins; C035026:SRPRA protein, human