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Evolutionary conservation of DNA-contact residues in DNA-binding domains.

Chang YL, Tsai HK, Kao CY, Chen YC, Hu YJ, Yang JM.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S3.PMID: 18541056 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.

Luscombe NM, Thornton JM.

J Mol Biol. 2002 Jul 26;320(5):991-1009.PMID: 12126620 [PubMed - indexed for MEDLINE]Related articles

Functional conservation of Rel binding sites in drosophilid genomes.

Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA.

Genome Res. 2007 Sep;17(9):1327-35.PMID: 17785540 [PubMed - indexed for MEDLINE]Related articlesFree article

Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity.

Raviscioni M, Gu P, Sattar M, Cooney AJ, Lichtarge O.

J Mol Biol. 2005 Jul 15;350(3):402-15.PMID: 15946684 [PubMed - indexed for MEDLINE]Related articles

Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases.

Lucas P, Otis C, Mercier JP, Turmel M, Lemieux C.

Nucleic Acids Res. 2001 Feb 15;29(4):960-9.PMID: 11160929 [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

An evolutionary trace method defines binding surfaces common to protein families.

Lichtarge O, Bourne HR, Cohen FE.

J Mol Biol. 1996 Mar 29;257(2):342-58.PMID: 8609628 [PubMed - indexed for MEDLINE]Related articles

Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.

Chen YC, Wu CY, Lim C.

Proteins. 2007 May 15;67(3):671-80.PMID: 17340633 [PubMed - indexed for MEDLINE]Related articles

Predicting DNA-binding sites of proteins from amino acid sequence.

Yan C, Terribilini M, Wu F, Jernigan RL, Dobbs D, Honavar V.

BMC Bioinformatics. 2006 May 19;7:262.PMID: 16712732 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative footprinting of DNA-binding proteins.

Contreras-Moreira B, Collado-Vides J.

Bioinformatics. 2006 Jul 15;22(14):e74-80.PMID: 16873524 [PubMed - indexed for MEDLINE]Related articlesFree article

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. Epub 2009 Jan 23.PMID: 19165315 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of DNA-binding proteins using support vector machines and evolutionary profiles.

Kumar M, Gromiha MM, Raghava GP.

BMC Bioinformatics. 2007 Nov 27;8:463.PMID: 18042272 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.

Polavarapu N, Mariño-Ramírez L, Landsman D, McDonald JF, Jordan IK.

BMC Genomics. 2008 May 17;9:226.PMID: 18485226 [PubMed - indexed for MEDLINE]Related articlesFree article

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

Mirny LA, Gelfand MS.

J Mol Biol. 2002 Aug 2;321(1):7-20.PMID: 12139929 [PubMed - indexed for MEDLINE]Related articles

Nomenclature of the ARID family of DNA-binding proteins.

Wilsker D, Probst L, Wain HM, Maltais L, Tucker PW, Moran E.

Genomics. 2005 Aug;86(2):242-51.PMID: 15922553 [PubMed - indexed for MEDLINE]Related articles

Prediction of DNA-binding residues from sequence.

Ofran Y, Mysore V, Rost B.

Bioinformatics. 2007 Jul 1;23(13):i347-53.PMID: 17646316 [PubMed - indexed for MEDLINE]Related articlesFree article

Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases.

Verkhivker GM.

Bioinformatics. 2006 Aug 1;22(15):1846-54. Epub 2006 May 23.PMID: 16720585 [PubMed - indexed for MEDLINE]Related articlesFree article

The modular organization of domain structures: insights into protein-protein binding.

del Sol A, Carbonell P.

PLoS Comput Biol. 2007 Dec;3(12):e239.PMID: 18069884 [PubMed - indexed for MEDLINE]Related articlesFree article

DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins.

Hwang S, Gou Z, Kuznetsov IB.

Bioinformatics. 2007 Mar 1;23(5):634-6. Epub 2007 Jan 19.PMID: 17237068 [PubMed - indexed for MEDLINE]Related articlesFree article

RNA-binding residues in sequence space: conservation and interaction patterns.

Spriggs RV, Jones S.

Comput Biol Chem. 2009 Oct;33(5):397-403. Epub 2009 Jul 28.PMID: 19700370 [PubMed - indexed for MEDLINE]Related articles