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Progress in the prediction of pKa values in proteins

✍ Scribed by Emil Alexov; Ernest L. Mehler; Nathan Baker; António M. Baptista; Yong Huang; Francesca Milletti; Jens Erik Nielsen; Damien Farrell; Tommy Carstensen; Mats H. M. Olsson; Jana K. Shen; Jim Warwicker; Sarah Williams; J. Michael Word

Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
203 KB
Volume
79
Category
Article
ISSN
0887-3585

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✦ Synopsis

Abstract

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.

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