ArticleProteins2016
Protein structure refinement via molecular-dynamics simulations: What works and what does not?
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- Integration of proteomics and bioinformatics in traumatic brain injury biomarker discovery.Biotechnologia · 2025Article
- Making Use of Averaging Methods in MODELLER for Protein Structure Prediction.International journal of molecular sciences · 2024Article
- HLA-EpiCheck: novel approach for HLA B-cell epitope prediction using 3D-surface patch descriptors derived from molecular dynamic simulations.Bioinformatics advances · 2024Article
- Repurposing Anti-Dengue Compounds against Monkeypox Virus Targeting Core Cysteine Protease.Biomedicines · 2023Article
- Article
- PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking.Synthetic and systems biotechnology · 2021Article
- Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?PLoS computational biology · 2021Article
- Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.Journal of chemical theory and computation · 2021Article
- Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction.Frontiers in molecular biosciences · 2021Article
- Bioluminescent Multi-Characteristic Opsin for Simultaneous Optical Stimulation and Continuous Monitoring of Cortical Activities.Frontiers in cellular neuroscience · 2021Article
- Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.Journal of chemical information and modeling · 2020Article
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 2020Article
- High-accuracy protein structures by combining machine-learning with physics-based refinement.Proteins · 2020Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- Driven to near-experimental accuracy by refinement via molecular dynamics simulations.Proteins · 2019Article
- Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.Journal of chemical theory and computation · 2019Article
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Protein structure refinement during CASP11 by the Feig group was described. Molecular dynamics simulations were used in combination with an improved selection and averaging protocol. On average, modest refinement was achieved with some targets improved significantly. Analysis of the CASP submission from our group focused on refinement success versus amount of sampling, refinement of different secondary structure elements and whether refinement varied as a function of which group provided initial models. The refinement of local stereochemical features was examined via the MolProbity score and an updated protocol was developed that can generate high-quality structures with very low MolProbity scores for most starting structures with modest computational effort. Proteins 2016; 84(Suppl 1):282-292. © 2015 Wiley Periodicals, Inc.
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