Modeling of metal interaction geometries for protein-ligand docking Export

@article{citeulike:2174996, abstract = {The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74\% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. Proteins 2007. {\copyright} 2007 Wiley-Liss, Inc.}, address = {University of Hamburg, Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany; Max-Planck-Institut f\"{u}r Informatik, Stuhlsatzenhausweg 85, 66123 Saarbr\"{u}cken, Germany}, author = {Seebeck, Birte and Reulecke, Ingo and K\"{a}mper, Andreas and Rarey, Matthias}, citeulike-article-id = {2174996}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.21818}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18041759}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18041759}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/117347077/ABSTRACT}, doi = {10.1002/prot.21818}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {docking, energy\_functions, flexx, metal}, number = {9999}, pages = {NA+}, posted-at = {2009-06-20 12:59:37}, priority = {2}, title = {Modeling of metal interaction geometries for protein-ligand docking}, url = {http://dx.doi.org/10.1002/prot.21818}, volume = {9999}, year = {2007} }

TY - JOUR ID - citeulike:2174996 L3 - citeulike-article-id:2174996 N2 - The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. Proteins 2007. © 2007 Wiley-Liss, Inc. IS - 9999 JF - Proteins: Structure, Function, and Bioinformatics AD - University of Hamburg, Center for Bioinformatics, Bundesstrasse 43, 20146 Hamburg, Germany; Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany TI - Modeling of metal interaction geometries for protein-ligand docking VL - 9999 SP - NA KW - docking KW - energy_functions KW - flexx KW - metal AU - Seebeck, Birte AU - Reulecke, Ingo AU - Kämper, Andreas AU - Rarey, Matthias PY - 2007/// UR - http://dx.doi.org/10.1002/prot.21818 ER -