ArticleBMC bioinformatics2010
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Drug Discovery forInternational journal of molecular sciences · 2021Review
- Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape ofFrontiers in molecular biosciences · 2021Review
- The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A Structure-Based Drug Discovery Paradigm.International journal of molecular sciences · 2019Review
- Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis.PLoS computational biology · 2016Article
- Crucial roles of single residues in binding affinity, specificity, and promiscuity in the cellulosomal cohesin-dockerin interface.The Journal of biological chemistry · 2015Article
- Amino acid distribution rules predict protein fold: protein grammar for beta-strand sandwich-like structures.Biomolecules · 2015Article
- Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics.International journal of molecular sciences · 2014Review
- Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling.Bioinformation · 2014Article
- Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.Journal of molecular evolution · 2011Article
- NCACO-score: an effective main-chain dependent scoring function for structure modeling.BMC bioinformatics · 2011Article
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4 authors.
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Abstract
backgroundAccurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design.
resultsHere we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 A for all residues and 0.73 A for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site http://bioinfo.weizmann.ac.il/hunter/ was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions.
conclusionsOur results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.
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