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...

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Bibliographic Details
Published in:Journal of chemical information and modeling Vol. 48; no. 8; p. 1616
Main Authors: Kerzmann, Andreas, Fuhrmann, Jan, Kohlbacher, Oliver, Neumann, Dirk
Format: Journal Article
Language:English
Published: United States 01.08.2008
Subjects:
Algorithms
Binding Sites
Calibration
Carbohydrate Metabolism
Carbohydrates - chemistry
Computational Biology - methods
Dimerization
Models, Molecular
Protein Binding
Protein Structure, Tertiary
Proteins - chemistry
Proteins - metabolism
Software Design
ISSN:1549-9596
Online Access:Get more information
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Summary: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.
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ISSN:1549-9596
DOI:10.1021/ci800103u