Multiscale characterization of protein conformational ensembles Export

@article{citeulike:4178196, abstract = {We propose a multiscale exploration method to characterize the conformational space populated by a protein at equilibrium. The method efficiently obtains a large set of equilibrium conformations in two stages: first exploring the entire space at a coarse-grained level of detail, then narrowing a refined exploration to selected low-energy regions. The coarse-grained exploration periodically adds all-atom detail to selected conformations to ensure that the search leads to regions which maintain low energies in all-atom detail. The second stage reconstructs selected low-energy coarse-grained conformations in all-atom detail. A low-dimensional energy landscape associated with all-atom conformations allows focusing the exploration to energy minima and their conformational ensembles. The lowest energy ensembles are enriched with additional all-atom conformations through further multiscale exploration. The lowest energy ensembles obtained from the application of the method to three different proteins correctly capture the known functional states of the considered systems. Proteins 2009. {\copyright} 2009 Wiley-Liss, Inc.}, address = {Department of Computer Science, Rice University, Houston, Texas 77005; Department of Bioengineering, Rice University, Houston, Texas 77005; Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030; Department of Chemistry, Rice University, Houston, Texas 77005}, author = {Shehu, Amarda and Kavraki, Lydia E. and Clementi, Cecilia}, citeulike-article-id = {4178196}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.22390}, citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/121675822/ABSTRACT}, doi = {10.1002/prot.22390}, issn = {1097-0134}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {clustering, coarse\_grain}, number = {4}, pages = {837--851}, posted-at = {2009-03-26 19:48:25}, priority = {2}, title = {Multiscale characterization of protein conformational ensembles}, url = {http://dx.doi.org/10.1002/prot.22390}, volume = {76}, year = {2009} }

TY - JOUR ID - citeulike:4178196 L3 - citeulike-article-id:4178196 N2 - We propose a multiscale exploration method to characterize the conformational space populated by a protein at equilibrium. The method efficiently obtains a large set of equilibrium conformations in two stages: first exploring the entire space at a coarse-grained level of detail, then narrowing a refined exploration to selected low-energy regions. The coarse-grained exploration periodically adds all-atom detail to selected conformations to ensure that the search leads to regions which maintain low energies in all-atom detail. The second stage reconstructs selected low-energy coarse-grained conformations in all-atom detail. A low-dimensional energy landscape associated with all-atom conformations allows focusing the exploration to energy minima and their conformational ensembles. The lowest energy ensembles are enriched with additional all-atom conformations through further multiscale exploration. The lowest energy ensembles obtained from the application of the method to three different proteins correctly capture the known functional states of the considered systems. Proteins 2009. © 2009 Wiley-Liss, Inc. IS - 4 JF - Proteins: Structure, Function, and Bioinformatics SN - 1097-0134 AD - Department of Computer Science, Rice University, Houston, Texas 77005; Department of Bioengineering, Rice University, Houston, Texas 77005; Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030; Department of Chemistry, Rice University, Houston, Texas 77005 EP - 851 TI - Multiscale characterization of protein conformational ensembles VL - 76 SP - 837 KW - clustering KW - coarse_grain AU - Shehu, Amarda AU - Kavraki, Lydia AU - Clementi, Cecilia PY - 2009/// UR - http://dx.doi.org/10.1002/prot.22390 ER -