On the evaluation and optimization of protein X-ray structures for pKa calculations.

ABSTRACT: The calculation of the physical properties of a protein from its X-ray structure is of importance in virtually every aspect of modern biology. Although computational algorithms have been developed for calculating everything from the dynamics of a protein to its binding specificity, only limited information is available on the ability of these methods to give accurate results when used with a particular X-ray structure. We examine the ability of a pKa calculation algorithm to predict the proton-donating residue in the catalytic mechanism of hen egg white lysozyme. We examine the correlation between the ability of the pKa calculation method to obtain the correct result and the overall characteristics of 41 X-ray structures such as crystallization conditions, resolution, and the output of str

SUBMITTER: Nielsen JE 

PROVIDER: S-EPMC2312414 | biostudies-literature | 2003 Feb

REPOSITORIES: biostudies-literature