Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction.

作者: Colin A. Smith , Tanja Kortemme

DOI: 10.1016/J.JMB.2008.05.023

关键词:

摘要: … We were interested in selectively sampling backbone motion in specified local regions of the protein while keeping other regions fixed. Therefore, we devised a flexible scheme for …

参考文章(55)
Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill, A kinematic view of loop closure. Journal of Computational Chemistry. ,vol. 25, pp. 510- 528 ,(2004) , 10.1002/JCC.10416
T. Kortemme, D. Baker, A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 99, pp. 14116- 14121 ,(2002) , 10.1073/PNAS.202485799
Kim T. Simons, Charles Kooperberg, Enoch Huang, David Baker, Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Journal of Molecular Biology. ,vol. 268, pp. 209- 225 ,(1997) , 10.1006/JMBI.1997.0959
Brent A. Appleton, Yingnan Zhang, Ping Wu, Jian Ping Yin, Walter Hunziker, Nicholas J. Skelton, Sachdev S. Sidhu, Christian Wiesmann, Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity. Journal of Biological Chemistry. ,vol. 281, pp. 22312- 22320 ,(2006) , 10.1074/JBC.M602901200
Carol A. Rohl, Charlie E.M. Strauss, Dylan Chivian, David Baker, Modeling structurally variable regions in homologous proteins with rosetta Proteins. ,vol. 55, pp. 656- 677 ,(2004) , 10.1002/PROT.10629
Elias Lolis, Tom Alber, Robert C. Davenport, David Rose, Fred C. Hartman, Gregory A. Petsko, Structure of yeast triosephosphate isomerase at 1.9-A resolution. Biochemistry. ,vol. 29, pp. 6609- 6618 ,(1990) , 10.1021/BI00480A009
Tanja Kortemme, Lukasz A Joachimiak, Alex N Bullock, Aaron D Schuler, Barry L Stoddard, David Baker, Computational redesign of protein-protein interaction specificity Nature Structural & Molecular Biology. ,vol. 11, pp. 371- 379 ,(2004) , 10.1038/NSMB749
Roland L. Dunbrack, Fred E. Cohen, Bayesian statistical analysis of protein side-chain rotamer preferences Protein Science. ,vol. 6, pp. 1661- 1681 ,(1997) , 10.1002/PRO.5560060807