ArticleProceedings of the National Academy of Sciences of the United States of America2013
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling.Pathogens (Basel, Switzerland) · 2024Article
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.Journal of chemical theory and computation · 2023Article
- AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes.Biomolecules · 2023Article
- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- 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
- Biomolecular modeling thrives in the age of technology.Nature computational science · 2021Article
- Residue-Level Contact Reveals Modular Domain Interactions of PICK1 Are Driven by Both Electrostatic and Hydrophobic Forces.Frontiers in molecular biosciences · 2020Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- 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
- Protein homology model refinement by large-scale energy optimization.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.Bioinformatics (Oxford, England) · 2016Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
- Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
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13 authors.
Funding
Abstract
The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our laboratory for the prediction of protein structure from amino acid sequence, is illustrated. Candidate models are selected, based on probabilities of the conformational families determined by multiplexed replica-exchange simulations, from the 10th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). For target T0663, classified as a new fold, which consists of two domains homologous to those of known proteins, UNRES predicted the correct symmetry of packing, in which the domains are rotated with respect to each other by 180° in the experimental structure. By contrast, models obtained by knowledge-based methods, in which each domain is modeled very accurately but not rotated, resulted in incorrect packing. Two UNRES models of this target were featured by the assessors. Correct domain packing was also predicted by UNRES for the homologous target T0644, which has a similar structure to that of T0663, except that the two domains are not rotated. Predictions for two other targets, T0668 and T0684_D2, are among the best ones by global distance test score. These results suggest that our physics-based method has substantial predictive power. In particular, it has the ability to predict domain-domain orientations, which is a significant advance in the state of the art.
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