Benchmarking pKa prediction

作者: Matthew N Davies , Christopher P Toseland , David S Moss , Darren R Flower

DOI: 10.1186/1471-2091-7-18

关键词:

摘要: Background pKa values are a measure of the protonation ionizable groups in proteins. Ionizable involved intra-protein, protein-solvent and protein-ligand interactions as well solubility, protein folding catalytic activity. The pKa shift group from its intrinsic value is determined by perturbation residue environment can be calculated three-dimensional structural data.

参考文章(37)
Paul R. Gooley, Max A. Keniry, Roumen A. Dimitrov, Danny E. Marsh, David W. Keizer, Kenwyn R. Gayler, Bruce R. Grant, The NMR solution structure and characterization of pH dependent chemical shifts of the beta-elicitin, cryptogein. Journal of Biomolecular NMR. ,vol. 12, pp. 523- 534 ,(1998) , 10.1023/A:1008395001008
Jack S. Cohen, John H. Griffin, Alan N. Schechter, Nuclear Magnetic Resonance Titration Curves of Histidine Ring Protons Journal of Biological Chemistry. ,vol. 248, pp. 4305- 4310 ,(1973) , 10.1016/S0021-9258(19)43773-3
Donald Bashford, An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules ISCOPE '97 Proceedings of the Scientific Computing in Object-Oriented Parallel Environments. pp. 233- 240 ,(1997)
Christopher P Toseland, Helen McSparron, Matthew N Davies, Darren R Flower, PPD v1.0—an integrated, web-accessible database of experimentally determined protein pKa values Nucleic Acids Research. ,vol. 34, pp. 199- 203 ,(2006) , 10.1093/NAR/GKJ035
Eugene Demchuk, Rebecca C. Wade, Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins The Journal of Physical Chemistry. ,vol. 100, pp. 17373- 17387 ,(1996) , 10.1021/JP960111D
X. Raquet, V. Lounnas, J. Lamotte-Brasseur, J.M. Frère, R.C. Wade, pKa calculations for class A beta-lactamases: methodological and mechanistic implications. Biophysical Journal. ,vol. 73, pp. 2416- 2426 ,(1997) , 10.1016/S0006-3495(97)78270-5