Progress in the prediction of pKa values in proteins

TY - JOUR

T1 - Progress in the prediction of pKa values in proteins

AU - Alexov, Emil

AU - Mehler, Ernest L.

AU - Baker, Nathan

AU - M. Baptista, António

AU - Huang, Yong

AU - Milletti, Francesca

AU - Erik Nielsen, Jens

AU - Farrell, Damien

AU - Carstensen, Tommy

AU - Olsson, Mats H. M.

AU - Shen, Jana K.

AU - Warwicker, Jim

AU - Williams, Sarah

AU - Word, J. Michael

PY - 2011/12

Y1 - 2011/12

N2 - 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 as 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.

AB - 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 as 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.

KW - pKa, protein electrostatics, pH dependent properties of proteins, predicting pKa values in proteins

U2 - 10.1002/prot.23189

DO - 10.1002/prot.23189

M3 - Journal article

SN - 0887-3585

VL - 79

SP - 3260

EP - 3275

JO - Proteins: Structure, Function, and Bioinformatics

JF - Proteins: Structure, Function, and Bioinformatics

IS - 12

ER -