ArticleComputational biology and chemistry2011
Direct correlation analysis improves fold recognition.
Article in Computational biology and chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 22 citations in OpenAlex.
- Protein contact prediction using metagenome sequence data and residual neural networks.Bioinformatics (Oxford, England) · 2020Article
- Exploring RNA conformational space under sparse distance restraints.Scientific reports · 2017Article
- Reduction, alignment and visualisation of large diverse sequence families.BMC bioinformatics · 2016Article
- The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance.Biophysical journal · 2015Article
- TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool.BMC bioinformatics · 2015Article
- Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel.PLoS computational biology · 2014Article
- Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.PloS one · 2014Article
- Emerging methods in protein co-evolution.Nature reviews. Genetics · 2013Review
- Article
- From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction.PLoS computational biology · 2013Article
- Protein topology from predicted residue contacts.Protein science : a publication of the Protein Society · 2012Article
- Article
- Structural constraints on the covariance matrix derived from multiple aligned protein sequences.PloS one · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The extraction of correlated mutations through the method of direct information (DI) provides predicted contact residue pairs that can be used to constrain the three dimensional structures of proteins. We apply this method to a large set of decoy protein folds consisting of many thousand well-constructed models, only tens of which have the correct fold. We find that DI is able to greatly improve the ranking of the true (native) fold but others still remain high scoring that would be difficult to discard due to small shifts in the core beta sheets.
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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.