BALLDock/SLICK: a new method for protein-carbohydrate docking.
Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We present a new docking method specifically designed to handle docking of carbohydrate-like compounds. BALLDock/SLICK combines an evolutionary docking algorithm for flexible ligands and flexible receptor side chains with carbohydrate-specific scoring and energy functions. The scoring function has been designed to identify accurate ligand poses, while the energy function yields accurate estimates of the binding free energies of these poses. On a test set of known protein-sugar complexes we demonstrate the ability of the approach to generate correct poses for almost all of the structures and achieve very low mean errors for the predicted binding free energies.
Kerzmann
Andreas
A
Division for Simulation of Biological Systems, Center for Bioinformatics, University of Tubingen, Sand 14, 72076 Tubingen, Germany.
Fuhrmann
Jan
J
Kohlbacher
Oliver
O
Neumann
Dirk
D
D000465:Algorithms; D001665:Binding Sites; D002138:Calibration; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D019281:Dimerization; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012985:Software Design
D002241:Carbohydrates; D011506:Proteins