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iGNM - Online service for Gaussian Network Model

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....

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iGNM - Online service for Gaussian Network Model | gnmdb.csb.pitt.edu Reviews

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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&#46...

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iGNM - Online service for Gaussian Network Model | gnmdb.csb.pitt.edu Reviews

https://gnmdb.csb.pitt.edu

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&#46...

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gnmdb.csb.pitt.edu

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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.

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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&#46...

3

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...

4

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 ...

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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...

btrportal.org

NIHBTR: Online Resources

http://www.btrportal.org/resources

Dataset / Database Additional Information. All Data Sizes -. O DSN6 format electron density map reader (.ds6, .dsn6, .omap). AMBER 'binpos' trajectory reader (.binpos). AMBER CRD trajectory reader (.crd, .crdbox). AMBER 4-6 structure file(.parm). AMBER 7-9 restart file(.rst7). AMBER 7-9 structure file(.prmtop, .parm7). AMBER NetCDF trajectory reader (.nc). Amira mesh, scalar. Analyze (.img.gz). ASL values of a single voxel. Autodock Grid Map File reader (.map). AVS Field File reader (.fld). GRASP surface...

gnm.csb.pitt.edu

DynOmics Portal 1.0 - Dynamics, Proteomics and Beyond

http://gnm.csb.pitt.edu/Theory_EnvENM.php

Environment GNM ( env. Gaussian Network Model (GNM. Is a powerful tool to sample conformational dynamics based on contact topology in a coarse-grained presentation. Here we present a method to consider protein dynamics in the presence of environment. Its GNM counterpart is first derived and implemented for the first time in this interface. GNM predictions that take account of crystal contacts have proven to yield more accurate B-factor predictions than conventional GNM. GNM can be derived as follows.

gnm.csb.pitt.edu

Dynomics Portal 1.0 - Dynamics Proteomics and Beyond

http://gnm.csb.pitt.edu/Tutorial.php

Dynamics of Structural Proteome and Beyond. Portal provides information on the equilibrium dynamics of biomolecular systems using as input structural data uploaded by users. At the core of. Portal are two elastic network models: the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM). Distinctive functionalities of. For the underlying theory and assumptions. 11 Query with Default options. 13 Considering Environmental Perturbations. 2 Default Results Page. 21 Molecular Motions Animations.

gnm.csb.pitt.edu

DynOmics Portal 1.0 - Dynamics, Proteomics and Beyond

http://gnm.csb.pitt.edu/index.php

What is the DynOmics. ENM server computes biomolecular systems dynamics for user-uploaded structural coordinates or PDB identifiers, by integrating two widely used elastic network models (ENMs) the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM). Unique features include the consideration of environment, the prediction of potential functional sites and reconstruction of all-atom conformers from deformed coarse-grained structures. For more information see Theory. Upload a local file:.

gnm.csb.pitt.edu

DynOmics Portal 1.0 - Dynamics, Proteomics and Beyond

http://gnm.csb.pitt.edu/References.php

1 Bahar,I., Atilgan,A.R. and Erman,B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. 2 Haliloglu,T., Bahar,I. and Erman,B. (1997) Gaussian dynamics of folded proteins. Phys Rev. Lett. 3 Atilgan,A.R., Durell,S.R., Jernigan,R.L., Demirel,M.C., Keskin,O. and Bahar,I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. 5 Ming, D. and Wall, M.E. (2005) Allostery in a coarse-grained model of protein dynamics. 11 Bahar,I...

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gnmdb.csb.pitt.edu

iGNM - Online service for Gaussian Network Model

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&#46...

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