title: Progress in the prediction of pKa values in proteins.
abstract: 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.
authors: Department of Physics, Clemson University, Clemson, SC, USA. ealexov@clemson.edu
authors: Emil
authors: E
authors: Alexov
authors: Ernest L
authors: EL
authors: Mehler
authors: Nathan
authors: N
authors: Baker
authors: António M
authors: AM
authors: Baptista
authors: Yong
authors: Y
authors: Huang
authors: Francesca
authors: F
authors: Milletti
authors: Jens Erik
authors: JE
authors: Nielsen
authors: Damien
authors: D
authors: Farrell
authors: Tommy
authors: T
authors: Carstensen
authors: Mats H M
authors: MH
authors: Olsson
authors: Jana K
authors: JK
authors: Shen
authors: Jim
authors: J
authors: Warwicker
authors: Sarah
authors: S
authors: Williams
authors: J Michael
authors: JM
authors: Word
mesh_terms: D019295:Computational Biology; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012106:Research; D055672:Static Electricity; D013223:Statistics as Topic / Q000379:methods
chemical_list: D011506:Proteins