Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics Export

@article{citeulike:1301465, abstract = {Summary The deformation patterns of a large set of representative proteins determined by essential dynamics extracted from atomistic simulations and coarse-grained normal mode analysis are compared. Our analysis shows that the deformational space obtained with both approaches is quite similar when taking into account a representative number of modes. The results provide not only a comprehensive validation of the use of a low-frequency modal spectrum to describe protein flexibility, but also a complete picture of normal mode limitations.}, author = {Rueda, Manuel and Chacon, Pablo and Orozco, Modesto}, citeulike-article-id = {1301465}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.str.2007.03.013}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17502102}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17502102}, citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6VSR-4NRCV6K-8/2/514235ac4bc30f8fa1087fc2b185456a}, comment = {This paper shows that B-factors computed out of NMA are similar with respect to the ones computed from dynamics (e.g. essential dynamics)}, day = {16}, doi = {10.1016/j.str.2007.03.013}, journal = {Structure}, keywords = {b-factors, comparison, flexibility, normal\_modes}, month = {May}, number = {5}, pages = {565--575}, posted-at = {2007-10-17 15:39:21}, priority = {2}, title = {Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics}, url = {http://dx.doi.org/10.1016/j.str.2007.03.013}, volume = {15}, year = {2007} }

TY - JOUR ID - citeulike:1301465 L3 - citeulike-article-id:1301465 N2 - Summary The deformation patterns of a large set of representative proteins determined by essential dynamics extracted from atomistic simulations and coarse-grained normal mode analysis are compared. Our analysis shows that the deformational space obtained with both approaches is quite similar when taking into account a representative number of modes. The results provide not only a comprehensive validation of the use of a low-frequency modal spectrum to describe protein flexibility, but also a complete picture of normal mode limitations. IS - 5 JF - Structure EP - 575 TI - Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics VL - 15 SP - 565 KW - b-factors KW - comparison KW - flexibility KW - normal_modes N1 - This paper shows that B-factors computed out of NMA are similar with respect to the ones computed from dynamics (e.g. essential dynamics) AU - Rueda, Manuel AU - Chacon, Pablo AU - Orozco, Modesto PY - 2007/05/16/ UR - http://dx.doi.org/10.1016/j.str.2007.03.013 ER -