Importance of Ligand Conformational Energies in Carbohydrate Docking: Sorting the Wheat from the Chaff

Overview

Journal J Comput Chem

Publisher Wiley

Specialties Biology
Chemistry

Date 2013 Dec 31

PMID 24375430

Citations 42

Authors

Anita K Nivedha

Spandana Makeneni

Bethany Lachele Foley

Matthew B Tessier

Robert J Woods

Affiliations

Soon will be listed here.

Abstract

Docking algorithms that aim to be applicable to a broad range of ligands suffer reduced accuracy because they are unable to incorporate ligand-specific conformational energies. Here, we develop a set of Carbohydrate Intrinsic (CHI) energy functions that quantify the conformational properties of oligosaccharides, based on the values of their glycosidic torsion angles. The relative energies predicted by the CHI energy functions mirror the conformational distributions of glycosidic linkages determined from a survey of oligosaccharide-protein complexes in the protein data bank. Addition of CHI energies to the standard docking scores in Autodock 3, 4.2, and Vina consistently improves pose ranking of oligosaccharides docked to a set of anticarbohydrate antibodies. The CHI energy functions are also independent of docking algorithm, and with minor modifications, may be incorporated into both theoretical modeling methods, and experimental NMR or X-ray structure refinement programs.

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