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Dirk Neumann and Oliver Kohlbacher (2010)

Structural Glycomics – Molecular Details of Protein-Carbohydrate Interactions and their Prediction

In: Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics, ed. by Martin G. Hicks and Carsten Kettner, Beilstein-Institut, Frankfurt, Germany.

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 discuss the peculiarities of protein-carbohydrate interactions and their impact on protein-carbohydrate docking and review the state of the art in docking of carbohydrates to proteins. Finally, we give an overview of carbohydrate docking
studies and 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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