ArticleBioinformatics (Oxford, England)2016
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Recapturing Cooperativity of α-Helix Formation and Packing in Coarse-Grained Protein Structure Modeling with Multitorsional Potentials.The journal of physical chemistry. B · 2025Article
- Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.Journal of chemical theory and computation · 2025Article
- Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.The journal of physical chemistry letters · 2023Review
- Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach.Biomolecules · 2023Article
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions.Frontiers in molecular biosciences · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study.Journal of chemical information and modeling · 2020Article
- Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.Journal of chemical information and modeling · 2020Article
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.PLoS computational biology · 2018Article
- A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.Journal of computational chemistry · 2018Article
- UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.Nucleic acids research · 2018Article
- Extension of coarse-grained UNRES force field to treat carbon nanotubes.Journal of molecular modeling · 2018Article
- Accelerating physical simulations of proteins by leveraging external knowledge.Wiley interdisciplinary reviews. Computational molecular scienceArticle
- Computational protein structure refinement: Almost there, yet still so far to go.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
17 authors.
Funding
Abstract
Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six single-domain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CαRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://www.unres.pl/ CONTACT: has5@cornell.edu.
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