ArticleNucleic acids research2016
iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Inferring dynamic information from protein structures by Gaussian integrals and deep learning.Bioinformatics (Oxford, England) · 2026Article
- Exploring the Hemoglobin T to R2 Path Using Gaussian Elastic Network Correlation Map Distance.Proteins · 2025Article
- Discrete protein dynamics enable long-range communication.bioRxiv : the preprint server for biology · 2025Article
- BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics.Protein science : a publication of the Protein Society · 2025Article
- Identifying a non-conserved site for achieving allosteric covalent inhibition of CECR2.Acta pharmacologica Sinica · 2025Article
- Structure-Based Identification of Non-covalent Prolyl Oligopeptidase 80 Inhibitors TargetingJournal of chemical information and modeling · 2025Article
- Decrypting Allostery in Membrane-Bound K-Ras4B Using ComplementaryJournal of the American Chemical Society · 2024Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- The effect of dimerization and ligand binding on the dynamics of Kaposi's sarcoma-associated herpesvirus protease.Proteins · 2022Article
- Helical structure motifs made searchable for functional peptide design.Nature communications · 2022Article
- Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis.The Journal of chemical physics · 2021Article
- Identification of Allosteric Effects in Proteins by Elastic Network Models.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Allosteric regulation of glutamate dehydrogenase deamination activity.Scientific reports · 2020Article
- Breaking a single hydrogen bond in the mitochondrial tRNAThe FEBS journal · 2020Article
- Rhapsody: predicting the pathogenicity of human missense variants.Bioinformatics (Oxford, England) · 2020Article
- Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.Biophysical journal · 2020Article
- Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations.Protein science : a publication of the Protein Society · 2020Article
- Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions.Computational and structural biotechnology journal · 2020Article
- Maximizing cohesion and separation for detecting protein functional modules in protein-protein interaction networks.PloS one · 2020Review
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
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4 authors.
Funding
Abstract
Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.
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