Preparation and refinement of model protein-ligand complexes.
The formation of ligand-protein complexes are critical for the correct functioning of a cell. The prediction of these interactions is important for our understanding of how the cell works and for the development of new drug molecules. Homology modeling is a method for predicting the structure of a protein based on a crystal structure template. Once a model of the protein is complete, a ligand-docking algorithm predicts the ligand-protein model interaction by searching for the best steric and energetically favorable fit. A refinement of the ligand-binding pocket improves the predicted interactions by considering the flexible nature of the ligand-binding pocket. In this chapter, we describe, from first principles, methods to identify and prepare the ligand-binding pocket in a protein model, to dock the ligand, and refine the resulting complex.
Molsoft L.L.C., San Diego, CA, USA. andy@molsoft.com
Andrew J W
AJ
Orry
Ruben
R
Abagyan
D000465:Algorithms; D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D009010:Monte Carlo Method; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D040681:Structural Homology, Protein
D008024:Ligands; D011506:Proteins