gnmdb.csb.pitt.edu
iGNM 2.0 - Gaussian Network Model database
http://gnmdb.csb.pitt.edu/References.php
Computational and Systems Biology. 1 Li,H., Chang,YY, Yang,LW and Bahar,I. (2016) iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. 2 Flory,P.J. (1976) Statistical thermodynamics of random networks. Proc R. Soc. Lond. A. 3 Bahar,I., Atilgan,A.R. and Erman,B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Phys Rev. Lett. Curr Opin. Struct. Biol. Chapman and Hall/CRC: Boca Raton, FL, pp. 41-64. WIREs Comput Mol Sci.
ignm.ccbb.pitt.edu
iGNM 2.0 - Gaussian Network Model database
http://ignm.ccbb.pitt.edu/References.php
Computational and Systems Biology. 1 Li,H., Chang,YY, Yang,LW and Bahar,I. (2016) iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. 2 Flory,P.J. (1976) Statistical thermodynamics of random networks. Proc R. Soc. Lond. A. 3 Bahar,I., Atilgan,A.R. and Erman,B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Phys Rev. Lett. Curr Opin. Struct. Biol. Chapman and Hall/CRC: Boca Raton, FL, pp. 41-64. WIREs Comput Mol Sci.
gnmdb.csb.pitt.edu
iGNM 2.0 - Gaussian Network Model database
http://gnmdb.csb.pitt.edu/GNM_Theory.php
Computational and Systems Biology. GAUSSIAN NETWORK MODEL (GNM). Schematic representation of equilibrium position vectors of residues, their distance vectors and fluctuations. Based on the statistical mechanical theory developed by Flory and coworkers for polymer gels. Where network junctions undergo Gaussian fluctuations. In the GNM, the positions of the network junctions/nodes are identified with the C. Carbons are separated by less than a cutoff distance R. Which is usually taken around 7. Is the GNM ...
ignm.ccbb.pitt.edu
iGNM - Online service for Gaussian Network Model
http://ignm.ccbb.pitt.edu/index.php
Computational and Systems Biology. What is the GNM DB? Which questions can be answered? Several studies in the last decade have drawn attention to the significance of intrinsic dynamics as a major determinant of the mechanism of action of proteins and their complexes (1-5). Intrinsic dynamics refers to conformational changes intrinsically favored by 3D structure, which often underlie the adaptation of biomolecules to functional interactions (6). Or which ones provide adequate flexibility. 2 Bahar,I.,...
gnmdb.csb.pitt.edu
iGNM 2.0 - Gaussian Network Model database
http://gnmdb.csb.pitt.edu/Tutorial.php
Computational and Systems Biology. Tutorial for Gaussian Network Model Database (GNM-DB) i. 11 Query single PDB. 2 Default Results page. 23 Domain Separations by Dynamics. 24 GNM Connectivity Model. 26 Collectivity of slow modes. 27 Results in plain text. 11 Query single PDB. ID (eg., 101M) and click the Go iGNM button to submit a query to GNM database. Both the GNM results for the. Is required. Please click the Run and Allow buttons to run Jmol when the security warning displayed below pops up:. 11 quer...
gnmdb.csb.pitt.edu
iGNM - Online service for Gaussian Network Model
http://gnmdb.csb.pitt.edu/index.php
Computational and Systems Biology. What is the GNM DB? Which questions can be answered? Several studies in the last decade have drawn attention to the significance of intrinsic dynamics as a major determinant of the mechanism of action of proteins and their complexes (1-5). Intrinsic dynamics refers to conformational changes intrinsically favored by 3D structure, which often underlie the adaptation of biomolecules to functional interactions (6). Or which ones provide adequate flexibility. 2 Dobbins,S....
