ArticleNucleic acids research2005
Predicting specificity-determining residues in two large eukaryotic transcription factor families.
Article in Nucleic acids research, 2005. 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.
- A deterministic code for transcription factor-DNA recognition through computation of binding interfaces.NAR genomics and bioinformatics · 2022Article
- Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease.Nucleic acids research · 2019Article
- Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors.Journal of molecular modeling · 2019Article
- The diversification of the basic leucine zipper family in eukaryotes correlates with the evolution of multicellularity.BMC evolutionary biology · 2016Article
- Computational learning on specificity-determining residue-nucleotide interactions.Nucleic acids research · 2015Article
- Overexpression of cAMP-response element modulator causes abnormal growth and development of the atrial myocardium resulting in a substrate for sustained atrial fibrillation in mice.International journal of cardiology · 2013Article
- SPEER-SERVER: a web server for prediction of protein specificity determining sites.Nucleic acids research · 2012Article
- Functionally important positions can comprise the majority of a protein's architecture.Proteins · 2011Article
- An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.Algorithms for molecular biology : AMB · 2010Article
- Multi-Harmony: detecting functional specificity from sequence alignment.Nucleic acids research · 2010Article
- Tradeoff between stability and multispecificity in the design of promiscuous proteins.PLoS computational biology · 2009Article
- Ensemble approach to predict specificity determinants: benchmarking and validation.BMC bioinformatics · 2009Article
- Combining specificity determining and conserved residues improves functional site prediction.BMC bioinformatics · 2009Article
- Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors.PloS one · 2009Article
- SDR: a database of predicted specificity-determining residues in proteins.Nucleic acids research · 2009Article
- Article
- An efficient method for statistical significance calculation of transcription factor binding sites.Bioinformation · 2007Article
- Background frequencies for residue variability estimates: BLOSUM revisited.BMC bioinformatics · 2007Article
- Functional specificity lies within the properties and evolutionary changes of amino acids.Journal of molecular biology · 2007Article
- Sequence harmony: detecting functional specificity from alignments.Nucleic acids research · 2007Article
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2 authors.
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Abstract
Certain amino acid residues in a protein, when mutated, change the protein's function. We present an improved method of finding these specificity-determining positions that uses all the protein sequence data available for a family of homologous proteins. We study in detail two families of eukaryotic transcription factors, basic leucine zippers and nuclear receptors, because of the large amount of sequences and experimental data available. These protein families also have a clear definition of functional specificity: DNA-binding specificity. We compare our results to three other methods, including the evolutionary trace algorithm and a method that depends on orthology relationships. All of the predictions are compared to the available mutational and crystallographic data. We find that our method provides superior predictions of the known specificity-determining residues and also predicts residue positions within these families that deserve further study for their roles in functional specificity.
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