ArticleProteins2019
Driven to near-experimental accuracy by refinement via molecular dynamics simulations.
Article in Proteins, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Cecropin A Improves the Antibacterial Activity of Hen Egg White Lysozyme against ChallengingPharmaceutics · 2022Article
- Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment.Proteins · 2021Article
- Article
- DeepRefiner: high-accuracy protein structure refinement by deep network calibration.Nucleic acids research · 2021Article
- Fast and effective protein model refinement using deep graph neural networks.Nature computational science · 2021Article
- Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy.International journal of molecular sciences · 2021Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Improved protein structure refinement guided by deep learning based accuracy estimation.Nature communications · 2021Article
- Contribution of machine learning approaches in response to SARS-CoV-2 infection.Informatics in medicine unlocked · 2021Review
- Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization.Computational and structural biotechnology journal · 2021Article
- Performance and Its Limits in Rigid Body Protein-Protein Docking.Structure (London, England : 1993) · 2020Article
- ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.Proteins · 2020Article
- High-accuracy protein structures by combining machine-learning with physics-based refinement.Proteins · 2020Article
- Improved protein structure prediction using predicted interresidue orientations.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- High-accuracy refinement using Rosetta in CASP13.Proteins · 2019Article
- Article
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3 authors.
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Abstract
Protein model refinement has been an essential part of successful protein structure prediction. Molecular dynamics simulation-based refinement methods have shown consistent improvement of protein models. There had been progress in the extent of refinement for a few years since the idea of ensemble averaging of sampled conformations emerged. There was little progress in CASP12 because conformational sampling was not sufficiently diverse due to harmonic restraints. During CASP13, a new refinement method was tested that achieved significant improvements over CASP12. The new method intended to address previous bottlenecks in the refinement problem by introducing new features. Flat-bottom harmonic restraints replaced harmonic restraints, sampling was performed iteratively, and a new scoring function and selection criteria were used. The new protocol expanded conformational sampling at reduced computational costs. In addition to overall improvements, some models were refined significantly to near-experimental accuracy.
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