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The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction.

Manning JR, Jefferson ER, Barton GJ.

BMC Bioinformatics. 2008 Jan 25;9:51.PMID: 18221517 [PubMed - indexed for MEDLINE]Related articlesFree article

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.PMID: 15647305 [PubMed - indexed for MEDLINE]Related articlesFree article

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.PMID: 14552658 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.

Pei J, Cai W, Kinch LN, Grishin NV.

Bioinformatics. 2006 Jan 15;22(2):164-71. Epub 2005 Nov 8.PMID: 16278237 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting residue-wise contact orders in proteins by support vector regression.

Song J, Burrage K.

BMC Bioinformatics. 2006 Oct 3;7:425.PMID: 17014735 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.

Aydin Z, Altunbasak Y, Borodovsky M.

BMC Bioinformatics. 2006 Mar 30;7:178.PMID: 16571137 [PubMed - indexed for MEDLINE]Related articlesFree article

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.

Chica C, Labarga A, Gould CM, López R, Gibson TJ.

BMC Bioinformatics. 2008 May 6;9:229.PMID: 18460207 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis and prediction of functional sub-types from protein sequence alignments.

Hannenhalli SS, Russell RB.

J Mol Biol. 2000 Oct 13;303(1):61-76.PMID: 11021970 [PubMed - indexed for MEDLINE]Related articles

Relating destabilizing regions to known functional sites in proteins.

Dessailly BH, Lensink MF, Wodak SJ.

BMC Bioinformatics. 2007 Apr 30;8:141.PMID: 17470296 [PubMed - indexed for MEDLINE]Related articlesFree article

REVCOM: a robust Bayesian method for evolutionary rate estimation.

Bordner AJ, Abagyan R.

Bioinformatics. 2005 May 15;21(10):2315-21. Epub 2005 Mar 4.PMID: 15749694 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.

Aytuna AS, Gursoy A, Keskin O.

Bioinformatics. 2005 Jun 15;21(12):2850-5. Epub 2005 Apr 26.PMID: 15855251 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.PMID: 17883866 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting functional sites with an automated algorithm suitable for heterogeneous datasets.

La D, Livesay DR.

BMC Bioinformatics. 2005 May 13;6:116.PMID: 15890082 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein secondary structure: entropy, correlations and prediction.

Crooks GE, Brenner SE.

Bioinformatics. 2004 Jul 10;20(10):1603-11. Epub 2004 Feb 26.PMID: 14988117 [PubMed - indexed for MEDLINE]Related articlesFree article

Residue conservation information for generating near-native structures in protein-protein docking.

Duan Y, Reddy BV, Kaznessis YN.

J Bioinform Comput Biol. 2006 Aug;4(4):793-806.PMID: 17007068 [PubMed - indexed for MEDLINE]Related articles

Improving position-specific predictions of protein functional sites using phylogenetic motifs.

Dukka BK, Livesay DR.

Bioinformatics. 2008 Oct 15;24(20):2308-16. Epub 2008 Aug 21.PMID: 18723520 [PubMed - indexed for MEDLINE]Related articlesFree article

AL2CO: calculation of positional conservation in a protein sequence alignment.

Pei J, Grishin NV.

Bioinformatics. 2001 Aug;17(8):700-12.PMID: 11524371 [PubMed - indexed for MEDLINE]Related articlesFree article

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments.

Tillier ER, Lui TW.

Bioinformatics. 2003 Apr 12;19(6):750-5.PMID: 12691987 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.

Najmanovich R, Kurbatova N, Thornton J.

Bioinformatics. 2008 Aug 15;24(16):i105-11.PMID: 18689810 [PubMed - indexed for MEDLINE]Related articlesFree article