ArticlePloS one2011
Structural constraints on the covariance matrix derived from multiple aligned protein sequences.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- Direct coupling analysis and the attention mechanism.BMC bioinformatics · 2025Article
- Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs.PLoS computational biology · 2018Article
- Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics.F1000Research · 2016Review
- Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor.PloS one · 2015Article
- Characteristics of protein residue-residue contacts and their application in contact prediction.Journal of molecular modeling · 2014Article
- A tale of two machines: a review of the BLAST meeting, Tucson, AZ, 20-24 January 2013.Molecular microbiology · 2014Review
- Coevolutionary signals across protein lineages help capture multiple protein conformations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Article
- Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions.Computational and structural biotechnology journal · 2013Review
- Prediction of contact residue pairs based on co-substitution between sites in protein structures.PloS one · 2013Article
- Prediction of protein contacts from correlated sequence substitutions.Science progress · 2013Review
- Deciphering membrane protein structures from protein sequences.Genome biology · 2012Article
- Protein topology from predicted residue contacts.Protein science : a publication of the Protein Society · 2012Article
- Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention.Pacific Symposium on Biocomputing. Pacific Symposium on BiocomputingArticle
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top 10 ranked models, with the current implementation, our summary statistic is the number of correct folds included in the top 10 models--which is on average over 50 percent.
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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.