ArticleBiophysical journal2006
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Transmembrane Prostate Androgen-Induced Protein 1 Molecular Modeling and Refinement Using Coarse-Grained Molecular Dynamics.ACS omega · 2025Article
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.International journal of molecular sciences · 2018Review
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- Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.PLoS computational biology · 2016Article
- iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.Nucleic acids research · 2016Article
- Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.Frontiers in molecular biosciences · 2016Article
- Large scale rigidity-based flexibility analysis of biomolecules.Structural dynamics (Melville, N.Y.) · 2016Article
- Cutoff lensing: predicting catalytic sites in enzymes.Scientific reports · 2015Article
- Specific non-local interactions are not necessary for recovering native protein dynamics.PloS one · 2014Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations.Bulletin of mathematical biology · 2013Article
- Elastic Network Models are Robust to Variations in Formalism.Journal of chemical theory and computation · 2012Article
- Are different stoichiometries feasible for complexes between lymphotoxin-alpha and tumor necrosis factor receptor 1?BMC structural biology · 2012Article
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- Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.Biophysical journal · 2012Article
- Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models.Biophysical journal · 2011Article
- Sequence composition and environment effects on residue fluctuations in protein structures.The Journal of chemical physics · 2010Article
- Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.Biophysical journal · 2010Article
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3 authors.
Funding
Abstract
Simple coarse-grained models, such as the Gaussian network model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to define residue interactions and introducing more than one interaction parameter between residues. We use B-factors from 98 ultra-high resolution (<or=1.0 A) x-ray crystal structures to optimize the interaction parameters. The average correlation between Gaussian network-model fluctuation predictions and the B-factors is 0.64 for the data set, consistent with a previous large-scale study. By separating residue interactions into covalent and noncovalent, we achieve an average correlation of 0.74, and addition of ligands and cofactors further improves the correlation to 0.75. However, further separating the noncovalent interactions into nonpolar, polar, and mixed yields no significant improvement. The addition of simple chemical information results in better prediction quality without increasing the size of the coarse-grained model.
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