Collective motions of rigid fragments in protein structures from smoothed electron density distributions.

@article{citeulike:2915126, abstract = {In this work, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM) approaches are applied to describe the dynamics of protein structure graphs built from calculated promolecular electron density (ED) distribution functions. A first set of analyses is carried out on results obtained from ED maxima calculated at various smoothing levels. A second set is achieved for ED networks whose edges are weighted by ED overlap integral values. Results are compared with those obtained through the classical GNM and ANM approaches applied to networks of C(alpha) atoms. It is shown how the network model and the consideration of crystal packing as well as of the side chains may lead to various improvements dependent upon the structure under study. The selected protein structures are Crambin and Pancreatic Trypsin Inhibitor because of their small size and numerous dynamical data obtained by other authors.}, address = {Laboratoire de Physico-Chimie Informatique (PCI), Groupe de Chimie Physique Th\'{e}orique et Structurale, University of Namur (FUNDP), Rue de Bruxelles 61, B-5000 Namur, Belgium. laurence.leherte@fundp.ac.be}, author = {Leherte, L. and Vercauteren, D. P. }, citeulike-article-id = {2915126}, doi = {http://dx.doi.org/10.1002/jcc.20908}, issn = {1096-987X}, journal = {Journal of computational chemistry}, keywords = {enm\_application\_d-enm}, month = {July}, number = {9}, pages = {1472--1489}, posted-at = {2008-06-22 14:10:44}, priority = {2}, title = {Collective motions of rigid fragments in protein structures from smoothed electron density distributions.}, url = {http://dx.doi.org/10.1002/jcc.20908}, volume = {29}, year = {2008} }

TY - JOUR ID - citeulike:2915126 L3 - citeulike-article-id:2915126 TI - Collective motions of rigid fragments in protein structures from smoothed electron density distributions. JF - Journal of computational chemistry VL - 29 IS - 9 SP - 1472 EP - 1489 AD - Laboratoire de Physico-Chimie Informatique (PCI), Groupe de Chimie Physique Théorique et Structurale, University of Namur (FUNDP), Rue de Bruxelles 61, B-5000 Namur, Belgium. laurence.leherte@fundp.ac.be SN - 1096-987X N2 - In this work, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM) approaches are applied to describe the dynamics of protein structure graphs built from calculated promolecular electron density (ED) distribution functions. A first set of analyses is carried out on results obtained from ED maxima calculated at various smoothing levels. A second set is achieved for ED networks whose edges are weighted by ED overlap integral values. Results are compared with those obtained through the classical GNM and ANM approaches applied to networks of C(alpha) atoms. It is shown how the network model and the consideration of crystal packing as well as of the side chains may lead to various improvements dependent upon the structure under study. The selected protein structures are Crambin and Pancreatic Trypsin Inhibitor because of their small size and numerous dynamical data obtained by other authors. KW - enm_application_d-enm AU - Leherte, L AU - Vercauteren, DP PY - 2008/07/15/ UR - http://dx.doi.org/10.1002/jcc.20908 ER -