An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD Export

@article{citeulike:2963571, abstract = {Abstract: A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking programs to reproduce experimentally observed binding modes. Three docking programs (Gold, Glide, and Fred) were used to generate poses for a set of 88 proteinligand complexes for which the crystal structure is known. The new criterion is based on the real space R-factor (RSR), which measures how well a group of atomsin our case the ligandfits the experimental electron density by comparing that density to the expected density, calculated from the model (i.e., the predicted ligand pose). The RSR-based measure is compared to the traditional criterion, the root-mean-square distance (RMSD) between the docking pose and the binding configuration in the crystallographic model. The results highlight several shortcomings of the RMSD criterion that do not affect the RSR-based measure. Examples illustrate that the RSR-derived approach allows a more meaningful a posteriori assessment of docking methods and results. Practical implications for docking evaluations and for methodological development work in this field are discussed.}, address = {AstraZeneca R\&D M\"{o}lndal, S-431 83 M\"{o}lndal, Sweden}, author = {Yusuf, Dilmurat and Davis, Andrew M. and Kleywegt, Gerard J. and Schmitt, Stefan}, citeulike-article-id = {2963571}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ci800084x}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci800084x}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18598022}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18598022}, day = {4}, doi = {10.1021/ci800084x}, journal = {J. Chem. Inf. Model.}, keywords = {benchmarks, density, docking, xray}, month = {July}, posted-at = {2009-06-17 11:31:29}, priority = {2}, title = {An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD}, url = {http://dx.doi.org/10.1021/ci800084x}, year = {2008} }

TY - JOUR ID - citeulike:2963571 L3 - citeulike-article-id:2963571 N2 - Abstract: A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking programs to reproduce experimentally observed binding modes. Three docking programs (Gold, Glide, and Fred) were used to generate poses for a set of 88 proteinligand complexes for which the crystal structure is known. The new criterion is based on the real space R-factor (RSR), which measures how well a group of atomsin our case the ligandfits the experimental electron density by comparing that density to the expected density, calculated from the model (i.e., the predicted ligand pose). The RSR-based measure is compared to the traditional criterion, the root-mean-square distance (RMSD) between the docking pose and the binding configuration in the crystallographic model. The results highlight several shortcomings of the RMSD criterion that do not affect the RSR-based measure. Examples illustrate that the RSR-derived approach allows a more meaningful a posteriori assessment of docking methods and results. Practical implications for docking evaluations and for methodological development work in this field are discussed. JF - J. Chem. Inf. Model. AD - AstraZeneca R&D Mölndal, S-431 83 Mölndal, Sweden TI - An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD KW - benchmarks KW - density KW - docking KW - xray AU - Yusuf, Dilmurat AU - Davis, Andrew AU - Kleywegt, Gerard AU - Schmitt, Stefan PY - 2008/07/04/ UR - http://dx.doi.org/10.1021/ci800084x ER -