The authors state that JEN is employed by Novozymes A/S.
The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins†
Article first published online: 15 OCT 2011
Copyright © 2011 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Special Issue: Protein Electrostatics Calculations: Critical Assessment of Progress and Problems
Volume 79, Issue 12, pages 3249–3259, December 2011
How to Cite
Nielsen, J. E., Gunner, M. R. and García-Moreno E., B. (2011), The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins, 79: 3249–3259. doi: 10.1002/prot.23194
- Issue published online: 10 NOV 2011
- Article first published online: 15 OCT 2011
- Accepted manuscript online: 14 SEP 2011 03:53PM EST
- Manuscript Received: 13 SEP 2011
- Manuscript Accepted: 13 SEP 2011
- NSF. Grant Number: MCB-1022208
- NIH. Grant Number: 5G12 RR03060
- NSF. Grant Number: MCB-0743422
- NIH. Grant Number: GM-061597
- NIH. Grant Number: GM-073838
- Science Foundation Ireland: President of Ireland Young Researcher award. Grant Number: 04/YI1/M537
- Research Frontiers award. Grant Number: 08/RFP/BIC1140
- pKa values;
- staphylococcal nuclease;
The pKa Cooperative (http://www.pkacoop.org) was organized to advance development of accurate and useful computational methods for structure-based calculation of pKa values and electrostatic energies in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational, and experimental studies of protein electrostatics. To improve structure-based energy calculations, it is necessary to better understand the physical character and molecular determinants of electrostatic effects. Thus, the Cooperative intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure-based electrostatics calculations. To help guide the development of computational methods, the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pKa values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site-directed mutagenesis. The pKa values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pKa values in water. Many computational methods were tested in this first Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to objectively assess the performance of many computational methods tested on this one extensive data set. This volume of Proteins: Structure, Function, and Bioinformatics introduces the pKa Cooperative, presents reports submitted by participants in the Blind Prediction Challenge, and highlights some of the problems in structure-based calculations identified during this exercise. Proteins 2011; © 2011 Wiley-Liss, Inc.