TY - GEN A1 - Baumeister, Timm A1 - Cordes, Frank T1 - A new Model for the Free Energy of Solvation and its Application in Protein Ligand Scoring N2 - A new and time efficient model to evaluate the free energy of solvation has been developed. The solvation free energy is separated into an electrostatic term, a hydrogen bond term, and a rest-term, combining both entropic and van der Waals effects. The electrostatic contribution is evaluated with a simplified boundary element method using the partial charges of the MMFF94 force field. The number of hydrogen bonds and the solvent excluded surface area over the surface atoms are used in a linear model to estimate the non-electrostatic contribution. This model is applied to a set of 213 small and mostly organic molecules, yielding an rmsd of 0.87kcal/mol and a correlation with experimental data of r=0.951. The model is applied as a supplementary component of the free energy of binding to estimate binding constants of protein ligand complexes. The intermolecular interaction energy is evaluated by using the MMFF94 force field. T3 - ZIB-Report - 04-51 KW - scoring KW - solvation KW - free energy Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8265 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Cordes, Frank A1 - Roitzsch, Rainer A1 - Schütte, Christof T1 - Identification of Molecular Conformations via Statistical Analysis of Simulation Data JF - Comp. Chem. Y1 - 1999 VL - 20 SP - 1760 EP - 1774 ER - TY - CHAP A1 - Wende, Florian A1 - Cordes, Frank A1 - Steinke, Thomas T1 - On Improving the Performance of Multi-threaded CUDA Applications with Concurrent Kernel Execution by Kernel Reordering T2 - Application Accelerators in High Performance Computing (SAAHPC), 2012 Symposium on Y1 - 2012 U6 - https://doi.org/10.1109/SAAHPC.2012.12 SP - 74 EP - 83 ER - TY - JOUR A1 - Guerler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2008 UR - http://www.sciencedirect.com/science/article/pii/S0303264707001670 U6 - https://doi.org/DOI: 10.1016/j.biosystems.2007.11.004 VL - 92 IS - 1 SP - 42 EP - 48 ER - TY - JOUR A1 - Huisinga, Wilhelm A1 - Best, Christoph A1 - Roitzsch, Rainer A1 - Schütte, Christof A1 - Cordes, Frank T1 - From Simulation Data to Conformational Ensembles JF - J. Comp. Chem. Y1 - 1999 VL - 20 IS - 16 SP - 1760 EP - 1774 ER - TY - CHAP A1 - Galliat, Tobias A1 - Deuflhard, Peter A1 - Roitzsch, Rainer A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Automatic Identification of Metastable Conformations via Self-Organized Neural Networks T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-00-51 IS - 24 PB - Springer ER - TY - CHAP A1 - Galliat, Tobias A1 - Deuflhard, Peter A1 - Roitzsch, Rainer A1 - Cordes, Frank T1 - Automatic identification of metastable conformations via self-organized neural networks T2 - Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling Y1 - 2002 ER - TY - JOUR A1 - Fischer, Alexander A1 - Cordes, Frank A1 - Schütte, Christof T1 - Hybrid Monte Carlo with Adaptive Temperature in Mixed–Canonical Ensemble: Efficient conformational analysis of RNA JF - J. Comp. Chem. Y1 - 1998 U6 - https://doi.org/10.1002/(SICI)1096-987X(19981130)19:15<1689::AID-JCC2>3.0.CO;2-J VL - 19 IS - 15 SP - 1689 EP - 1697 ER - TY - CHAP A1 - Fischer, Alexander A1 - Schütte, Christof A1 - Deuflhard, Peter A1 - Cordes, Frank ED - Schlick, T. ED - Gan, H. T1 - Hierarchical Uncoupling-Coupling of Metastable Conformations T2 - Computational Methods for Macromolecules Y1 - 2002 UR - http://www.zib.de/PaperWeb/abstracts/ZR-01-03 IS - 24 SP - 235 EP - 259 PB - Springer ER - TY - JOUR A1 - Gürler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2007 ER -