The role and application of in silico docking in chemical genomics research.
In silico docking techniques are being used to investigate the complementarity at the molecular level of a ligand and a protein target. As such, docking studies can be used to identify the structural features that are important for binding and for in silico screening efforts in which suitable binding partners can be identified. Here we describe a practical approach for setting up docking simulations using different docking programs. We also cover the analysis and rescoring of the obtained docking poses. Possible pitfalls in the docking studies are discussed and hints are provided to resolve commonly occurring problems.
Jongejan
Aldo
A
Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
de Graaf
Chris
C
Vermeulen
Nico P E
NP
Leurs
Rob
R
de Esch
Iwan J P
IJ
D001665:Binding Sites; D002616:Chemical Engineering; D030562:Databases, Protein; D015195:Drug Design; D023281:Genomics; D006859:Hydrogen / Q000737:chemistry; D008024:Ligands; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D014867:Water / Q000737:chemistry
D008024:Ligands; D011506:Proteins; D014867:Water; D006859:Hydrogen