GARD: A Generally Applicable Replacement for RMSD Export

@article{BaberTCH09, abstract = {The root-mean-squared deviation (rmsd) is a widely used measure of distance between two aligned objects − often chemical structures. However, rmsd has a number of known limitations including difficulty of interpretation, no limit on weighting for any portion of the alignment, and a lack of normalization. In this work, a Generally Applicable Replacement for rmsD (GARD) is proposed. In this implementation atomic contributions are weighted by their relative importance to binding, as determined statistically by Andrews et al.(1), and as such this method is 'chemically aware'. This novel measure is normalized and does not have many of the failings of traditional rmsd. It is, thus, perfectly suited for a wide variety of uses, including the assessment of the quality of poses produced from molecular docking programs and the comparison of conformers. Rmsd and GARD are compared in their ability to assess docking software and multiple examples of the use of GARD to rescue essentially correct poses with a high rmsd are presented.}, author = {Baber, J. Christian and Thompson, David C. and Cross, Jason B. and Humblet, Christine}, citeulike-article-id = {5216835}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ci9001074}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci9001074}, day = {24}, doi = {10.1021/ci9001074}, journal = {Journal of Chemical Information and Modeling}, keywords = {alignment, binding, deviation, docking, gard, importance, interpretation, limitations, measure, normalization, poses, rmsd}, month = {August}, number = {8}, pages = {1889--1900}, posted-at = {2009-07-27 13:26:00}, priority = {2}, title = {GARD: A Generally Applicable Replacement for RMSD}, url = {http://dx.doi.org/10.1021/ci9001074}, volume = {49}, year = {2009} }

TY - JOUR ID - BaberTCH09 L3 - citeulike-article-id:5216835 N2 - The root-mean-squared deviation (rmsd) is a widely used measure of distance between two aligned objects − often chemical structures. However, rmsd has a number of known limitations including difficulty of interpretation, no limit on weighting for any portion of the alignment, and a lack of normalization. In this work, a Generally Applicable Replacement for rmsD (GARD) is proposed. In this implementation atomic contributions are weighted by their relative importance to binding, as determined statistically by Andrews et al.(1), and as such this method is ‘chemically aware’. This novel measure is normalized and does not have many of the failings of traditional rmsd. It is, thus, perfectly suited for a wide variety of uses, including the assessment of the quality of poses produced from molecular docking programs and the comparison of conformers. Rmsd and GARD are compared in their ability to assess docking software and multiple examples of the use of GARD to rescue essentially correct poses with a high rmsd are presented. IS - 8 JF - Journal of Chemical Information and Modeling EP - 1900 TI - GARD: A Generally Applicable Replacement for RMSD VL - 49 SP - 1889 KW - alignment KW - binding KW - deviation KW - docking KW - gard KW - importance KW - interpretation KW - limitations KW - measure KW - normalization KW - poses KW - rmsd AU - Baber, Christian AU - Thompson, David AU - Cross, Jason AU - Humblet, Christine PY - 2009/08/24/ UR - http://dx.doi.org/10.1021/ci9001074 ER -