SLICK--scoring and energy functions for protein-carbohydrate interactions.
Protein-carbohydrate interactions are increasingly being recognized as essential for many important biomolecular recognition processes. From these, numerous biomedical applications arise in areas as diverse as drug design, immunology, or drug transport. We introduce SLICK, a package containing a scoring and an energy function, which were specifically designed to predict binding modes and free energies of sugars and sugarlike compounds to proteins. SLICK accounts for van der Waals interactions, solvation effects, electrostatics, hydrogen bonds, and CH...pi interactions, the latter being a particular feature of most protein-carbohydrate interactions. Parameters for the empirical energy function were calibrated on a set of high-resolution crystal structures of protein-sugar complexes with known experimental binding free energies. We show that SLICK predicts the binding free energies of predicted complexes (through molecular docking) with high accuracy. SLICK is available as part of our molecular modeling package BALL (www.ball-project.org).
Kerzmann
Andreas
A
Division for Simulation of Biological Systems, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany. kerzmann@informatik.uni-tuebingen.de
Neumann
Dirk
D
Kohlbacher
Oliver
O
D002138:Calibration; D002241:Carbohydrates / Q000737:chemistry*; D003460:Crystallization; D015195:Drug Design; D006860:Hydrogen Bonding; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity
D002241:Carbohydrates; D011506:Proteins