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Progress in the prediction of p K a values in proteins
Author(s) -
Alexov Emil,
Mehler Ernest L.,
Baker Nathan,
M. Baptista António,
Huang Yong,
Milletti Francesca,
Erik Nielsen Jens,
Farrell Damien,
Carstensen Tommy,
Olsson Mats H. M.,
Shen Jana K.,
Warwicker Jim,
Williams Sarah,
Word J. Michael
Publication year - 2011
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.23189
Subject(s) - double blind , computer science , function (biology) , computational biology , medicine , biology , genetics , pathology , alternative medicine , placebo
The p K a ‐cooperative aims to provide a forum for experimental and theoretical researchers interested in protein p K a values and protein electrostatics in general. The first round of the p K a ‐cooperative, which challenged computational labs to carry out blind predictions against p K 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 p K a calculations, emphasizing methods that were used by the participants in calculating the blind p K 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 p K a calculations. Proteins 2011; © 2011 Wiley‐Liss, Inc.