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.
mmbios.org
MMBioS Software
http://www.mmbios.org/index.php/software
NIH Biomedical Technology and Research Resource (BTRR). Technology Research and Development. EAB Meeting Fall 2015. EAB Meeting Fall 2014. EAB Meeting Fall 2013. How to Acknowledge Us. The following software tools and services, developed by MMBioS partners, are freely available to the biomedical community. We ask that any publications resulting from their use include an acknowledgement. Elastic Network Models (ENM). CellBlender is a Blender addon for creation, simulation, visualization, and analysis of r...
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.,...
csb.pitt.edu
Joseph C. Ayoob | Computational & Systems Biology
http://www.csb.pitt.edu/people/faculty/joseph-c-ayoob
Computational and Systems Biology. Computational Biology Ph.D. TECBio REU @ Pitt. Joseph C. Ayoob. James R. Faeder. Robin E. C. Lee. Daniel M. Zuckerman. Molecular Biophysics Structural Biology. Microbiology & Molecular Genetics. Joseph C. Ayoob. Joseph C. Ayoob, Ph.D. PhD, Neuroscience, Johns Hopkins University School of Medicine; B.A. Biology, University of Pennsylvania. 3053 Biomedical Science Tower 3. Pittsburgh, PA 15213Phone: (412) 648-8646. Chennubhotla C (2012) First Steps. Chak K, Andreone BJ, O...
csb.pitt.edu
Ivet Bahar (Chair) | Computational & Systems Biology
http://www.csb.pitt.edu/people/faculty/ivet-bahar
Computational and Systems Biology. Computational Biology Ph.D. TECBio REU @ Pitt. Joseph C. Ayoob. James R. Faeder. Robin E. C. Lee. Daniel M. Zuckerman. Molecular Biophysics Structural Biology. Microbiology & Molecular Genetics. Ivet Bahar, Ph.D. Distinguished Professor and John K. Vries Chair. PhD in Chemistry, Istanbul Technical Institute; B.S. and M.S. in Chemical Engineering, Bogazici U. 3058 Biomedical Science Tower 3. Pittsburgh, PA 15213. Epub ahead of print]. Gur M, Zomot E, Cheng MH, 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...