ArticleAlgorithms for molecular biology : AMB2007
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.
Article in Algorithms for molecular biology : AMB, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Motifs in SARS-CoV-2 evolution.RNA (New York, N.Y.) · 2023Article
- Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.eLife · 2022Article
- Fast and accurate inference of gene regulatory networks through robust precision matrix estimation.Bioinformatics (Oxford, England) · 2022Article
- Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus.Virus evolution · 2020Article
- Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.PLoS computational biology · 2018Article
- Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections.F1000Research · 2017Article
- I-COMS: Interprotein-COrrelated Mutations Server.Nucleic acids research · 2015Article
- Assembly constraints drive co-evolution among ribosomal constituents.Nucleic acids research · 2015Article
- A new ensemble coevolution system for detecting HIV-1 protein coevolution.Biology direct · 2015Article
- Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis.Biomolecules · 2013Article
- Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis.BMC bioinformatics · 2012Article
- Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern.BMC evolutionary biology · 2012Article
- Integrated analysis of residue coevolution and protein structure in ABC transporters.PloS one · 2012Article
- Direct-coupling analysis of residue coevolution captures native contacts across many protein families.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- The coevolution of phycobilisomes: molecular structure adapting to functional evolution.Comparative and functional genomics · 2011Article
- Functional co-evolutionary study of glucosamine-6-phosphate synthase in mycoses causing fungi.Bioinformation · 2011Article
- Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.PLoS computational biology · 2010Article
- Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation.PloS one · 2010Article
- Computing and visually analyzing mutual information in molecular co-evolution.BMC bioinformatics · 2010Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSome amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues - coevolution. Our goal is to find these coevolving residues.
resultsWe present six new methods for detecting coevolving residues. Among other things, we suggest measures that are variants of Mutual Information, and measures that use a multidimensional representation of each residue in order to capture the physico-chemical similarities between amino acids. We created a benchmarking system, in silico, able to evaluate these methods through a wide range of realistic conditions. Finally, we use the combination of different methods as a way of improving performance.
conclusionOur best method (Row and Column Weighed Mutual Information) has an estimated accuracy increase of 63% over Mutual Information. Furthermore, we show that the combination of different methods is efficient, and that the methods are quite sensitive to the different conditions tested.
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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.