From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes

@article{citeulike:1665269, abstract = {Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time-scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all-atom protein structures starting from the C? atom positions, as obtained for instance from extensive coarse-grain simulations. The method, a reconstruction algorithm for coarse-grain structures (RACOGS), is validated by reconstructing ensembles of coarse-grain structures obtained during folding simulations of the proteins src-SH3 and S6. The results show that RACOGS consistently produces low energy, all-atom structures. A comparison of the free energy landscapes calculated using the coarse-grain structures versus the all-atom structures shows good correspondence and little distortion in the protein folding landscape. Proteins 2007. {\copyright} 2007 Wiley-Liss, Inc.}, address = {Department of Computer Science, Rice University, Houston, Texas 77005; Department of Bioengineering, Rice University, Houston, Texas 77005; Department of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030; Department of Chemistry, Rice University, Houston, Texas 77005}, author = {Heath, Allison P. and Kavraki, Lydia E. and Clementi, Cecilia}, citeulike-article-id = {1665269}, doi = {10.1002/prot.21371}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {coarse\_grain, protein\_structure}, number = {3}, pages = {646--661}, posted-at = {2008-09-26 18:14:38}, priority = {3}, title = {From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes}, url = {http://dx.doi.org/10.1002/prot.21371}, volume = {68}, year = {2007} }

TY - JOUR ID - citeulike:1665269 L3 - citeulike-article-id:1665269 N2 - Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time-scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all-atom protein structures starting from the C? atom positions, as obtained for instance from extensive coarse-grain simulations. The method, a reconstruction algorithm for coarse-grain structures (RACOGS), is validated by reconstructing ensembles of coarse-grain structures obtained during folding simulations of the proteins src-SH3 and S6. The results show that RACOGS consistently produces low energy, all-atom structures. A comparison of the free energy landscapes calculated using the coarse-grain structures versus the all-atom structures shows good correspondence and little distortion in the protein folding landscape. Proteins 2007. © 2007 Wiley-Liss, Inc. IS - 3 JF - Proteins: Structure, Function, and Bioinformatics AD - Department of Computer Science, Rice University, Houston, Texas 77005; Department of Bioengineering, Rice University, Houston, Texas 77005; Department of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030; Department of Chemistry, Rice University, Houston, Texas 77005 EP - 661 TI - From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes VL - 68 SP - 646 KW - coarse_grain KW - protein_structure AU - Heath, Allison AU - Kavraki, Lydia AU - Clementi, Cecilia PY - 2007/// UR - http://dx.doi.org/10.1002/prot.21371 ER -