Very fast empirical prediction and rationalization of protein pKa values.

@article{citeulike:1774899, abstract = {A very fast empirical method is presented for structure-based protein pKa prediction and rationalization. The desolvation effects and intra-protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root-mean-square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values.}, address = {Department of Chemistry, Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA.}, author = {Li, H. and Robertson, A. D. and Jensen, J. H. }, citeulike-article-id = {1774899}, doi = {10.1002/prot.20660}, issn = {1097-0134}, journal = {Proteins}, keywords = {bioinf\_methods, md\_simulation, pka}, month = {December}, number = {4}, pages = {704--721}, posted-at = {2008-04-25 20:55:37}, priority = {2}, title = {Very fast empirical prediction and rationalization of protein pKa values.}, url = {http://dx.doi.org/10.1002/prot.20660}, volume = {61}, year = {2005} }

TY - JOUR ID - citeulike:1774899 L3 - citeulike-article-id:1774899 TI - Very fast empirical prediction and rationalization of protein pKa values. JF - Proteins VL - 61 IS - 4 SP - 704 EP - 721 AD - Department of Chemistry, Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA. SN - 1097-0134 N2 - A very fast empirical method is presented for structure-based protein pKa prediction and rationalization. The desolvation effects and intra-protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root-mean-square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values. KW - bioinf_methods KW - md_simulation KW - pka AU - Li, H AU - Robertson, AD AU - Jensen, JH PY - 2005/12/01/ UR - http://dx.doi.org/10.1002/prot.20660 ER -