ArticleProteins2016
Assessment of refinement of template-based models in CASP11.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
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- 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
- High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment.International journal of biological macromolecules · 2020Article
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- Evaluation of model refinement in CASP13.Proteins · 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
- Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model.Protein science : a publication of the Protein Society · 2018Article
- Protein structure prediction.International journal of modern physics. B · 2018Article
- Modeling protein folding in vivo.Biology direct · 2018Article
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- Protein homology model refinement by large-scale energy optimization.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- PREFMD: a web server for protein structure refinement via molecular dynamics simulations.Bioinformatics (Oxford, England) · 2018Article
- What makes it difficult to refine protein models further via molecular dynamics simulations?Proteins · 2018Article
- Assessment of the model refinement category in CASP12.Proteins · 2018Article
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2 authors.
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Abstract
CASP11 (the 11th Meeting on the Critical Assessment of Protein Structure Prediction) ran a blind experiment in the refinement of protein structure predictions, the fourth such experiment since CASP8. As with the previous experiments, the predictors were provided with one starting structure from the server models of each of a selected set of template-based modeling targets and asked to refine the coordinates of the starting structure toward native. We assessed the refined structures with the Z-scores of the standard CASP measures, which compare the model-target similarities of the models from all the predictors. Furthermore, we assessed the refined structures with "relative measures," which compare the improvement in accuracy of each model with respect to the starting structure. The latter provides an assessment of the extent to which each predictor group is able to improve the starting structures toward native. We utilized heat maps to display improvements in the Calpha-Calpha distance matrix for each model. The heat maps labeled with each element of secondary structure helped us to identify regions of refinement toward native in each model. Most positively scoring models show modest improvements in multiple regions of the structure, while in some models we were able to identify significant repositioning of N/C-terminal segments and internal elements of secondary structure. The best groups were able to improve more than 70% of the targets from the starting models, and by an average of 3-5% in the standard CASP measures. Proteins 2016; 84(Suppl 1):260-281. © 2016 Wiley Periodicals, Inc.
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