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Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.

Gouveia-Oliveira R, Pedersen AG.

Algorithms Mol Biol. 2007 Oct 3;2:12.PMID: 17915013 [PubMed]Related articlesFree article

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information.

Buslje CM, Santos J, Delfino JM, Nielsen M.

Bioinformatics. 2009 May 1;25(9):1125-31. Epub 2009 Mar 10.PMID: 19276150 [PubMed - indexed for MEDLINE]Related articles

Reducing the false positive rate in the non-parametric analysis of molecular coevolution.

Codoñer FM, O'Dea S, Fares MA.

BMC Evol Biol. 2008 Apr 10;8:106.PMID: 18402697 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.

Little DY, Chen L.

PLoS One. 2009;4(3):e4762. Epub 2009 Mar 10.PMID: 19274093 [PubMed - indexed for MEDLINE]Related articlesFree article

Detecting coevolution in and among protein domains.

Yeang CH, Haussler D.

PLoS Comput Biol. 2007 Nov;3(11):e211. Epub 2007 Sep 18.PMID: 17983264 [PubMed - indexed for MEDLINE]Related articlesFree article

A Novel Method to Detect Proteins Evolving at Correlated Rates: Identifying New Functional Relationships between Coevolving Proteins.

Clark NL, Aquadro CF.

Mol Biol Evol. 2009 Dec 31. [Epub ahead of print]PMID: 20044587 [PubMed - as supplied by publisher]Related articles

The human protein coevolution network.

Tillier ER, Charlebois RL.

Genome Res. 2009 Oct;19(10):1861-71. Epub 2009 Aug 20.PMID: 19696150 [PubMed - indexed for MEDLINE]Related articles

Prediction of protein-protein binding site by using core interface residue and support vector machine.

Li N, Sun Z, Jiang F.

BMC Bioinformatics. 2008 Dec 22;9:553.PMID: 19102736 [PubMed - indexed for MEDLINE]Related articlesFree article

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

Shamim MT, Anwaruddin M, Nagarajaram HA.

Bioinformatics. 2007 Dec 15;23(24):3320-7. Epub 2007 Nov 7.PMID: 17989092 [PubMed - indexed for MEDLINE]Related articlesFree article

Integration of evolutionary features for the identification of functionally important residues in major facilitator superfamily transporters.

Jeon J, Yang JS, Kim S.

PLoS Comput Biol. 2009 Oct;5(10):e1000522. Epub 2009 Oct 2.PMID: 19798434 [PubMed - indexed for MEDLINE]Related articlesFree article

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.

Caporaso JG, Smit S, Easton BC, Hunter L, Huttley GA, Knight R.

BMC Evol Biol. 2008 Dec 3;8:327.PMID: 19055758 [PubMed - indexed for MEDLINE]Related articlesFree article

An amino acid map of inter-residue contact energies using metric multi-dimensional scaling.

Rakshit S, Ananthasuresh GK.

J Theor Biol. 2008 Jan 21;250(2):291-7. Epub 2007 Sep 26.PMID: 17981305 [PubMed - indexed for MEDLINE]Related articles

Sequence based residue depth prediction using evolutionary information and predicted secondary structure.

Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L.

BMC Bioinformatics. 2008 Sep 20;9:388.PMID: 18803867 [PubMed - indexed for MEDLINE]Related articlesFree article

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods.

Hnizdo V, Tan J, Killian BJ, Gilson MK.

J Comput Chem. 2008 Jul 30;29(10):1605-14.PMID: 18293293 [PubMed - indexed for MEDLINE]Related articlesFree article

Detecting groups of coevolving positions in a molecule: a clustering approach.

Dutheil J, Galtier N.

BMC Evol Biol. 2007 Nov 30;7:242.PMID: 18053141 [PubMed - indexed for MEDLINE]Related articlesFree article

Using evolutionary information to find specificity-determining and co-evolving residues.

Kolesov G, Mirny LA.

Methods Mol Biol. 2009;541:421-48. Review.PMID: 19381538 [PubMed - indexed for MEDLINE]Related articles

Safety and nutritional assessment of GM plants and derived food and feed: the role of animal feeding trials.

EFSA GMO Panel Working Group on Animal Feeding Trials.

Food Chem Toxicol. 2008 Mar;46 Suppl 1:S2-70. Epub 2008 Feb 13. Review.PMID: 18328408 [PubMed - indexed for MEDLINE]Related articles

Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis.

Miotto O, Heiny A, Tan TW, August JT, Brusic V.

BMC Bioinformatics. 2008;9 Suppl 1:S18.PMID: 18315849 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of the residue-residue coevolution network and the functionally important residues in proteins.

Lee BC, Park K, Kim D.

Proteins. 2008 Aug 15;72(3):863-72.PMID: 18275083 [PubMed - indexed for MEDLINE]Related articles

Automated alphabet reduction for protein datasets.

Bacardit J, Stout M, Hirst JD, Valencia A, Smith RE, Krasnogor N.

BMC Bioinformatics. 2009 Jan 6;10:6.PMID: 19126227 [PubMed - indexed for MEDLINE]Related articlesFree article