ArticlePLoS computational biology2013
Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 29 citations in OpenAlex.
- Deciphering SHP-2 conformational switching via elastic network models and transfer entropy analysis.Journal of molecular modeling · 2026Article
- Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference.Systematic biology · 2026Article
- Biotite: new tools for a versatile Python bioinformatics library.BMC bioinformatics · 2023Article
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Why are large conformational changes well described by harmonic normal modes?Biophysical journal · 2021Article
- Inferring functional units in ion channel pores via relative entropy.European biophysics journal : EBJ · 2021Article
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- Simple mechanics of protein machines.Journal of the Royal Society, Interface · 2019Article
- Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.International journal of molecular sciences · 2018Review
- Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis.The journal of physical chemistry. B · 2016Article
- Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.Proteins · 2016Article
- Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.PloS one · 2015Article
- Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations.Frontiers in plant science · 2015Review
- Integrating protein structural dynamics and evolutionary analysis with Bio3D.BMC bioinformatics · 2014Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained descriptions of protein dynamics, as an alternative to more computationally expensive approaches. In particular, the elastic network model, in which residue motions are subjected to pairwise harmonic potentials, is known to capture essential aspects of conformational dynamics in proteins, but has so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. We propose, for the first time, a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.
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