ArticleBMC biophysics2016
Evaluation of the coarse-grained OPEP force field for protein-protein docking.
Article in BMC biophysics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies.Current atherosclerosis reports · 2023Review
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2020Article
- Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr.Biophysical journal · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Article
- HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.Physical chemistry chemical physics : PCCP · 2017Article
- Multiscale simulation of molecular processes in cellular environments.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2016Review
- Review
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3 authors.
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Abstract
backgroundKnowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensional structure of a protein-protein complex. Docking itself only produces plausible candidate structures, which must be ranked using scoring functions to identify the structures that are most likely to occur in nature.
methodsIn this work, we rescore rigid body protein-protein predictions using the optimized potential for efficient structure prediction (OPEP), which is a coarse-grained force field. Using a force field based on continuous functions rather than a grid-based scoring function allows the introduction of protein flexibility during the docking procedure. First, we produce protein-protein predictions using ZDOCK, and after energy minimization via OPEP we rank them using an OPEP-based soft rescoring function. We also train the rescoring function for different complex classes and demonstrate its improved performance for an independent dataset.
resultsThe trained rescoring function produces a better ranking than ZDOCK for more than 50 % of targets, rising to over 70 % when considering only enzyme/inhibitor complexes.
conclusionsThis study demonstrates for the first time that energy functions derived from the coarse-grained OPEP force field can be employed to rescore predictions for protein-protein complexes.
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