ArticleProteins2011
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- Protein docking model evaluation by 3D deep convolutional neural networks.Bioinformatics (Oxford, England) · 2020Article
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Knowledge-based entropies improve the identification of native protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Protein structure prediction using residue- and fragment-environment potentials in CASP11.Proteins · 2016Article
- Distributions of experimental protein structures on coarse-grained free energy landscapes.The Journal of chemical physics · 2015Article
- GENN: a GEneral Neural Network for learning tabulated data with examples from protein structure prediction.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Redundancy-weighting for better inference of protein structural features.Bioinformatics (Oxford, England) · 2014Article
- Towards comprehensive analysis of protein family quantitative stability-flexibility relationships using homology models.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Energy functions in de novo protein design: current challenges and future prospects.Annual review of biophysics · 2013Review
- Effective inter-residue contact definitions for accurate protein fold recognition.BMC bioinformatics · 2012Article
- Article
- 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
- Evaluation of residue-residue contact predictions in CASP9.Proteins · 2011Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
Multibody 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. Our goal was to combine long range multibody potentials and short range potentials to improve recognition of native structure among misfolded decoys. We optimized the weights for four-body nonsequential, four-body sequential, and short range potentials to obtain optimal model ranking results for threading and have compared these data against results obtained with other potentials (26 different coarse-grained potentials from the Potentials 'R'Us web server have been used). Our optimized multibody potentials outperform all other contact potentials in the recognition of the native structure among decoys, both for models from homology template-based modeling and from template-free modeling in CASP8 decoy sets. We have compared the results obtained for this optimized coarse-grained potentials, where each residue is represented by a single point, with results obtained by using the DFIRE potential, which takes into account atomic level information of proteins. We found that for all proteins larger than 80 amino acids our optimized coarse-grained potentials yield results comparable to those obtained with the atomic DFIRE potential.
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