ArticleProteins2014
Evaluation of residue-residue contact prediction in CASP10.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Emerging frontiers in protein structure prediction following the AlphaFold revolution.Journal of the Royal Society, Interface · 2025Review
- Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN).The protein journal · 2022Article
- Improved Protein Structure Prediction Using a New Multi-Scale Network and Homologous Templates.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Article
- Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations.Cell reports methods · 2021Article
- Deep Learning in Protein Structural Modeling and Design.Patterns (New York, N.Y.) · 2020Review
- Chasing coevolutionary signals in intrinsically disordered proteins complexes.Scientific reports · 2020Article
- Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading.Scientific reports · 2020Article
- Analysis of several key factors influencing deep learning-based inter-residue contact prediction.Bioinformatics (Oxford, England) · 2020Article
- StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map.Scientific reports · 2019Article
- Article
- Assessing the accuracy of contact predictions in CASP13.Proteins · 2019Article
- Statistical investigations of protein residue direct couplings.PLoS computational biology · 2018Article
- DNCON2: improved protein contact prediction using two-level deep convolutional neural networks.Bioinformatics (Oxford, England) · 2018Article
- Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age.Proteins · 2018Article
- Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank.PloS one · 2018Article
- Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Forecasting residue-residue contact prediction accuracy.Bioinformatics (Oxford, England) · 2017Article
- RRCRank: a fusion method using rank strategy for residue-residue contact prediction.BMC bioinformatics · 2017Article
- An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences.Acta crystallographica. Section D, Structural biology · 2017Review
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Authors and funding
5 authors.
Funding
Abstract
We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.
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