ArticleProteins2016
Evaluation of free modeling targets in CASP11 and ROLL.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- ProtSeqGen: a novel deep learning model for protein sequence design.BMC bioinformatics · 2026Article
- Fast and accurate Ab Initio Protein structure prediction using deep learning potentials.PLoS computational biology · 2022Article
- VInternational journal of molecular sciences · 2022Review
- Article
- Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions.Nature communications · 2021Article
- MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction.Scientific reports · 2021Article
- Automated and optimally FRET-assisted structural modeling.Nature communications · 2020Article
- Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13.Proteins · 2019Article
- Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13.Proteins · 2019Article
- Article
- ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.Bioinformatics (Oxford, England) · 2019Article
- Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families.Genome biology · 2019Article
- Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins.Virology journal · 2019Article
- Improved fragment-based protein structure prediction by redesign of search heuristics.Scientific reports · 2018Article
- Article
- Evaluation of the template-based modeling in CASP12.Proteins · 2018Article
- Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solvent.Proteins · 2018Article
- Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.Proteins · 2018Article
- Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.Proteins · 2018Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
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5 authors.
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Abstract
We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51-66. © 2015 Wiley Periodicals, Inc.
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