Progress in the prediction of p Kavalues in proteins

Abstract

The p Ka‐cooperative aims to provide a forum for experimental and theoretical researchers interested in protein p Ka values and protein electrostatics in general. The first round of the p Ka‐cooperative, which challenged computational labs to carry out blind predictions against p Ka 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 Ka calculations, emphasizing methods that were used by the participants in calculating the blind p Ka 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 Ka calculations. Proteins 2011; © 2011 Wiley‐Liss, Inc.