ArticleProteins2011
CASP9 target classification.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 91 citations in OpenAlex.
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- Petabase-Scale Homology Search for Structure Prediction.Cold Spring Harbor perspectives in biology · 2024Review
- To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units.Proteins · 2023Article
- The transformative power of transformers in protein structure prediction.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Petascale Homology Search for Structure Prediction.bioRxiv : the preprint server for biology · 2023Article
- Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14).Proteins · 2021Article
- Continuous Automated Model EvaluatiOn (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods.Proteins · 2021Article
- Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14).Proteins · 2021Article
- Probabilistic divergence of a template-based modelling methodology from the ideal protocol.Journal of molecular modeling · 2021Article
- Article
- Comparative analysis of methods for evaluation of protein models against native structures.Bioinformatics (Oxford, England) · 2019Article
- DeepSF: deep convolutional neural network for mapping protein sequences to folds.Bioinformatics (Oxford, England) · 2018Article
- Evaluation of the template-based modeling in CASP12.Proteins · 2018Article
- CASP 11 target classification.Proteins · 2016Article
- Evaluation of free modeling targets in CASP11 and ROLL.Proteins · 2016Article
- Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
The Critical assessment of protein structure prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain-based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence-related templates and high server prediction performance were classified as TMB, whereas those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (five target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds.
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Registered trials
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.