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Blind, one-eyed, or eagle-eyed? pKa calculations during blind predictions with staphylococcal nuclease


  • The authors state no conflict of interest.


In the current contribution, the performance of Poisson–Boltzmann-based pKa calculations of SNase mutants as part of a blind prediction exercise facilitated by the pKa cooperative (“pKa_coop”) is described. A one parameter setting (“quick&dirty” approach) is used to provide an industry perspective where strong time constraints are frequently encountered. On the one hand, results are analyzed in terms of root mean square deviation performance. Furthermore, the pKa calculations are assessed for their ability to properly assign protonation state. For this purpose, a new measure called BIPS (binary protonation state at physiological pH) is introduced. Significant differences were found with both comparison measures based on the class of residues examined. In addition, the performance of PROPKA3 as well as the NULL model is examined on the same data set. Finally, pKa calculations on SNase mutants with available structural information have been performed and provide support for our calculation methods. The performance on this subset is better than on the pKa cooperative mutation data. In the pKa_coop data, no structural information on the generated mutants is available. This suggests the occurrence of a substantial structural rearrangement on the insertion of additional charged groups into SNase, which leads to improved prediction quality. Proteins 2011;. © 2011 Wiley-Liss, Inc.