ArticleJournal of chemical theory and computation2006
The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models.
Article in Journal of chemical theory and computation, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Functional Protein Dynamics Directly from Sequences.The journal of physical chemistry. B · 2023Article
- Structural compliance: A new metric for protein flexibility.Proteins · 2020Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.Biophysical journal · 2019Article
- Protocols for Molecular Dynamics Simulations of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.Protein science : a publication of the Protein Society · 2016Article
- Elastic network models capture the motions apparent within ensembles of RNA structures.RNA (New York, N.Y.) · 2014Article
- Computational and experimental characterization of RNA cubic nanoscaffolds.Methods (San Diego, Calif.) · 2014Article
- Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.The journal of physical chemistry. B · 2014Article
- Biomolecular dynamics: order-disorder transitions and energy landscapes.Reports on progress in physics. Physical Society (Great Britain) · 2012Article
- Elastic network normal modes provide a basis for protein structure refinement.The Journal of chemical physics · 2012Article
- The importance of slow motions for protein functional loops.Physical biology · 2012Article
- Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.Journal of structural and functional genomics · 2011Article
- MAVENs: motion analysis and visualization of elastic networks and structural ensembles.BMC bioinformatics · 2011Article
- Immunoglobulin Structure Exhibits Control over CDR Motion.Immunome research · 2011Article
- Models to Approximate the Motions of Protein Loops.Journal of chemical theory and computation · 2010Article
- Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease.Biophysical journal · 2010Article
- Comparing interfacial dynamics in protein-protein complexes: an elastic network approach.BMC structural biology · 2010Article
- Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.PLoS computational biology · 2010Article
- Temperature dependence of fluctuations in HIV1-protease.European biophysics journal : EBJ · 2010Article
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5 authors.
Funding
Abstract
Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode analysis for multiple scales on a high-resolution protein data set using various cutoff radii to define the residues considered to be interacting, or the extent of cooperativity of their motions. These scales include the residue-, atomic-, proton-, and explicit solvent-levels. Interestingly, atomic, proton, and explicit solvent level calculations all provide similar results at the same cutoff value, with the computed mean-square fluctuations showing only a slightly higher correlation (0.61) with the experimental temperature factors from crystallography than the results of the residue-level coarse-graining. The qualitative behavior of each level of coarse graining is similar at different cutoff values. The correlations between these fluctuations and the number of internal contacts improve with increased cutoff values. Our results demonstrate that atomic level elastic network models provide an improved representation for the collective motions of proteins compared to the coarse-grained models.
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