Progress in the prediction of pKa values in proteins

被引：214

作者：

Alexov, Emil ^{[1
]}

Mehler, Ernest L. ^{[2
]}

Baker, Nathan ^{[3
]}

Baptista, Antonio M. ^{[4
]}

Huang, Yong ^{[5
]}

Milletti, Francesca ^{[6
]}

Nielsen, Jens Erik ^{[7
]}

Farrell, Damien ^{[7
]}

Carstensen, Tommy ^{[7
]}

Olsson, Mats H. M. ^{[8
]}

Shen, Jana K. ^{[9
]}

Warwicker, Jim ^{[10
]}

Williams, Sarah ^{[11
]}

Word, J. Michael ^{[12
]}

机构：

[1] Clemson Univ, Dept Phys, Clemson, SC 29634 USA

[2] Cornel Univ, Weill Med Coll, New York, NY USA

[3] Pacific NW Natl Lab, Richland, WA 99352 USA

[4] Univ Nova Lisboa, Inst Tecnol Quim & Biol, P-1200 Lisbon, Portugal

[5] Washington Univ, Dept Biochem & Mol Biophys, St Louis, MO USA

[6] Univ Perugia, I-06100 Perugia, Italy

[7] Univ Coll Dublin, Sch Biomol & Biomed Sci, Dublin 2, Ireland

[8] Univ Copenhagen, Dept Chem, DK-1168 Copenhagen, Denmark

[9] Univ Oklahoma, Dept Chem & Biochem, Norman, OK 73019 USA

[10] Univ Manchester, Fac Life Sci, Manchester M13 9PL, Lancs, England

[11] Univ Calif San Diego, San Diego, CA 92103 USA

[12] OpenEye Sci Software Inc, Santa Fe, NM USA

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2011年 / 79卷 / 12期

关键词：

pKa; protein electrostatics; pH dependent properties of proteins; predicting pKa values in proteins; PH MOLECULAR-DYNAMICS; POISSON-BOLTZMANN EQUATION; MULTIPLE-SITE TITRATION; ADAPTIVE FAST MULTIPOLE; GENERALIZED BORN MODEL; CONSTANT-PH; ELECTROSTATIC INTERACTIONS; DIELECTRIC-CONSTANTS; IONIZABLE GROUPS; FREE-ENERGY;

D O I：

10.1002/prot.23189

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Proteins 2011; 79:3260-3275. (C) 2011 Wiley-Liss, Inc.

引用

页码：3260 / 3275

页数：16

共 127 条

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