Development and validation of a modular, extensible docking program: DOCK 5. Export

@article{citeulike:986216, abstract = {We report on the development and validation of a new version of DOCK. The algorithm has been rewritten in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools. We validated the sampling algorithm with a test set of 114 protein-ligand complexes. Using an optimized parameter set, we are able to reproduce the crystal ligand pose to within 2 A of the crystal structure for 79\% of the test cases using our rigid ligand docking algorithm with an average run time of 1 min per complex and for 72\% of the test cases using our flexible ligand docking algorithm with an average run time of 5 min per complex. Finally, we perform an analysis of the docking failures in the test set and determine that the sampling algorithm is generally sufficient for the binding pose prediction problem for up to 7 rotatable bonds; i.e. 99\% of the rigid ligand docking cases and 95\% of the flexible ligand docking cases are sampled successfully. We point out that success rates could be improved through more advanced modeling of the receptor prior to docking and through improvement of the force field parameters, particularly for structures containing metal-based cofactors.}, address = {Joint Graduate Program in Bioengineering, University of California, San Francisco, 600 16th Street, Genentech Hall, Box 2240, San Francisco, CA, 94143, USA.}, author = {Moustakas, Demetri T. and Lang, P T. and Pegg, Scott and Pettersen, Eric and Kuntz, Irwin D. and Brooijmans, Natasja and Rizzo, Robert C.}, citeulike-article-id = {986216}, citeulike-linkout-0 = {http://dx.doi.org/10.1007/s10822-006-9060-4}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17149653}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17149653}, day = {6}, doi = {10.1007/s10822-006-9060-4}, issn = {0920-654X}, journal = {J Comput Aided Mol Des}, keywords = {docking\_design}, month = {December}, posted-at = {2007-01-11 19:15:50}, priority = {2}, title = {Development and validation of a modular, extensible docking program: DOCK 5.}, url = {http://dx.doi.org/10.1007/s10822-006-9060-4}, year = {2006} }

TY - JOUR ID - citeulike:986216 L3 - citeulike-article-id:986216 N2 - We report on the development and validation of a new version of DOCK. The algorithm has been rewritten in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools. We validated the sampling algorithm with a test set of 114 protein-ligand complexes. Using an optimized parameter set, we are able to reproduce the crystal ligand pose to within 2 A of the crystal structure for 79% of the test cases using our rigid ligand docking algorithm with an average run time of 1 min per complex and for 72% of the test cases using our flexible ligand docking algorithm with an average run time of 5 min per complex. Finally, we perform an analysis of the docking failures in the test set and determine that the sampling algorithm is generally sufficient for the binding pose prediction problem for up to 7 rotatable bonds; i.e. 99% of the rigid ligand docking cases and 95% of the flexible ligand docking cases are sampled successfully. We point out that success rates could be improved through more advanced modeling of the receptor prior to docking and through improvement of the force field parameters, particularly for structures containing metal-based cofactors. JF - J Comput Aided Mol Des SN - 0920-654X AD - Joint Graduate Program in Bioengineering, University of California, San Francisco, 600 16th Street, Genentech Hall, Box 2240, San Francisco, CA, 94143, USA. TI - Development and validation of a modular, extensible docking program: DOCK 5. KW - docking_design AU - Moustakas, Demetri AU - Lang, P AU - Pegg, Scott AU - Pettersen, Eric AU - Kuntz, Irwin AU - Brooijmans, Natasja AU - Rizzo, Robert PY - 2006/12/06/ UR - http://dx.doi.org/10.1007/s10822-006-9060-4 ER -