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Proteins. 2011 Dec;79(12):3260-75. doi: 10.1002/prot.23189. Epub 2011 Oct 15.

Progress in the prediction of pKa values in proteins.

Author information

1
Department of Physics, Clemson University, Clemson, SC, USA. ealexov@clemson.edu

Abstract

The pK(a) -cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pK(a) values and protein electrostatics in general. The first round of the pK(a) -cooperative, which challenged computational labs to carry out blind predictions against pK(a) s experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6-10, 2009). This article serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. Here, we briefly outline existing approaches for pK(a) calculations, emphasizing methods that were used by the participants in calculating the blind pK(a) values in the first round of the cooperative. We then point out some of the difficulties encountered by the participating groups in making their blind predictions, and finally try to provide some insights for future developments aimed at improving the accuracy of pK(a) calculations.

PMID:
22002859
PMCID:
PMC3243943
DOI:
10.1002/prot.23189
[Indexed for MEDLINE]
Free PMC Article
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