ArticleJournal of structural and functional genomics2011
Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.
Article in Journal of structural and functional genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Interpreting human genetic variation at atomic resolution.Nature genetics · 2026Review
- Advancing Deep Variant Phenotyping of Mitochondrial Enzyme Complexes For Precision Medicine in Allogeneic Hematopoietic Stem-Cell Transplantation.Transplantation reports · 2025Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- Knowledge-based entropies improve the identification of native protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Distributions of experimental protein structures on coarse-grained free energy landscapes.The Journal of chemical physics · 2015Article
- Many-body effect in ion binding to RNA.The Journal of chemical physics · 2014Article
- Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method.PLoS computational biology · 2014Article
- Article
- Elastic network normal modes provide a basis for protein structure refinement.The Journal of chemical physics · 2012Article
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Authors and funding
6 authors.
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Abstract
We propose a novel method of calculation of free energy for coarse grained models of proteins by combining our newly developed multibody potentials with entropies computed from elastic network models of proteins. Multi-body potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Combining four-body non-sequential, four-body sequential and pairwise short range potentials with optimized weights for each term, our coarse-grained potential improved recognition of native structure among misfolded decoys, outperforming all other contact potentials for CASP8 decoy sets and performance comparable to the fully atomic empirical DFIRE potentials. By combing statistical contact potentials with entropies from elastic network models of the same structures we can compute free energy changes and improve coarse-grained modeling of protein structure and dynamics. The consideration of protein flexibility and dynamics should improve protein structure prediction and refinement of computational models. This work is the first to combine coarse-grained multibody potentials with an entropic model that takes into account contributions of the entire structure, investigating native-like decoy selection.
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