Andreas Kerzmann

Publications

• 3.88

  Impact points

  BALLDock/SLICK: a new method for protein-carbohydrate docking.

  Andreas Kerzmann, Jan Fuhrmann, Oliver Kohlbacher, Dirk Neumann

  Journal of chemical information and modeling. 08/2008; 48(8):1616-25.

  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... [more] 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.

• SLICK -- new methods for protein-carbohydrate docking

  Andreas Kerzmann

  01/2006

  Degree: Dr. rer. nat.

  Supervisor: Prof. Dr. Oliver Kohlbacher

• High Accuracy Prediction of Protein-Carbohydrate Interactions

  A. Kerzmann, D. Neumann, O. Kohlbacher

  21st International Lectin Meeting (Interlec 21), Shonan Village, Japan; 01/2004

• Modelling the Sugar-Lectin Interaction by Computer Simulated Docking

  D. Neumann, A. Kerzmann, O. Kohlbacher

  20th International Lectin Meeting (Interlec 20), Copenhagen, Denmark; 01/2002

• Calculation of Contact Forces

  G. Hotz, A. Kerzmann, C. Lennerz, R. Schmid, E. Schömer, T. Warken

  ACM Symposium on Virtual Reality Software and Technology; 01/1999

• Zwangsbasierte Dynamiksimulation im R2 unter Verwendung von Kreiskanten

  Andreas Kerzmann

  01/1999

  Degree: Diplom-Informatiker

  Supervisor: Prof. Dr. Günter Hotz, Prof. Dr. Elmar Schömer

• SiLVIA - a simulation library for virtual reality applications

  G. Hotz, A. Kerzmann, C. Lennerz, R. Schmid, E. Schömer, T. Warken

  IEEE Virtual Reality; 01/1999
• 3.88

  Impact points

  SLICK--scoring and energy functions for protein-carbohydrate interactions.

  Andreas Kerzmann, Dirk Neumann, Oliver Kohlbacher

  Journal of chemical information and modeling. 46(4):1635-42.

  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 sco... [more] 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).