ArticleProteins2014
Assessment of template-free modeling in CASP10 and ROLL.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 100 citations in OpenAlex.
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- Deep learning for protein secondary structure prediction: Pre and post-AlphaFold.Computational and structural biotechnology journal · 2022Review
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- Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions.Nature communications · 2021Article
- Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure.BMC bioinformatics · 2020Article
- Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.Journal of chemical information and modeling · 2020Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.The journal of physical chemistry. B · 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
- Approaches to ab initio molecular replacement of α-helical transmembrane proteins.Acta crystallographica. Section D, Structural biology · 2017Article
- RRCRank: a fusion method using rank strategy for residue-residue contact prediction.BMC bioinformatics · 2017Article
- Protein structural motifs in prediction and design.Current opinion in structural biology · 2017Review
- Article
- Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.Proteins · 2016Article
- Evaluation of free modeling targets in CASP11 and ROLL.Proteins · 2016Article
- Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
We present the assessment of predictions for Template-Free Modeling in CASP10 and a report on the first ROLL experiment wherein predictions are collected year round for review at the regular CASP season. Models were first clustered so that duplicated or very similar ones were grouped together and represented by one model in the cluster. The representatives were then compared with targets using GDT_TS, QCS, and three additional superposition-independent score functions newly developed for CASP10. For each target, the top 15 representatives by each score were pooled to form the Top15Union set. All models in this set were visually inspected by four of us independently using the new plugin, EvalScore, which we developed with the UCSF Chimera group. The best models were selected for each target after extensive debate among the four examiners. Groups were ranked by the number of targets (hits) for which a group's model was selected as one of the best models. The Keasar group had most hits in both categories, with four of 19 FM and eight of 36 ROLL targets. The most successful prediction servers were QUARK from Zhang's group for FM category with three hits and Zhang-server for the ROLL category with seven hits. As observed in CASP9, many successful groups were not true "template-free" modelers but used remote templates and/or server models to obtain their winning models. The results of the first ROLL experiment were broadly similar to those of the CASP10 FM exercise.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.