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Probabilistic annotation of protein sequences based on functional classifications.

Levy ED, Ouzounis CA, Gilks WR, Audit B.

BMC Bioinformatics. 2005 Dec 14;6:302.PMID: 16354297 [PubMed - indexed for MEDLINE]Related articlesFree article

A sequence alignment-independent method for protein classification.

Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I.

Appl Bioinformatics. 2004;3(2-3):137-48.PMID: 15693739 [PubMed - indexed for MEDLINE]Related articles

CORRIE: enzyme sequence annotation with confidence estimates.

Audit B, Levy ED, Gilks WR, Goldovsky L, Ouzounis CA.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S3.PMID: 17570146 [PubMed - indexed for MEDLINE]Related articlesFree article

Euclidian space and grouping of biological objects.

Grishin VN, Grishin NV.

Bioinformatics. 2002 Nov;18(11):1523-34.PMID: 12424125 [PubMed - indexed for MEDLINE]Related articlesFree article

CLUSS: clustering of protein sequences based on a new similarity measure.

Kelil A, Wang S, Brzezinski R, Fleury A.

BMC Bioinformatics. 2007 Aug 4;8:286.PMID: 17683581 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

Wilson CA, Kreychman J, Gerstein M.

J Mol Biol. 2000 Mar 17;297(1):233-49.PMID: 10704319 [PubMed - indexed for MEDLINE]Related articles

Blast sampling for structural and functional analyses.

Friedrich A, Ripp R, Garnier N, Bettler E, Deléage G, Poch O, Moulinier L.

BMC Bioinformatics. 2007 Feb 23;8:62.PMID: 17319945 [PubMed - indexed for MEDLINE]Related articlesFree article

A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins.

Mihalek I, Res I, Lichtarge O.

Bioinformatics. 2006 Jan 15;22(2):149-56. Epub 2005 Nov 22.PMID: 16303797 [PubMed - indexed for MEDLINE]Related articlesFree article

Application of a simple likelihood ratio approximant to protein sequence classification.

Kaján L, Kertész-Farkas A, Franklin D, Ivanova N, Kocsor A, Pongor S.

Bioinformatics. 2006 Dec 1;22(23):2865-9. Epub 2006 Nov 7.PMID: 17090576 [PubMed - indexed for MEDLINE]Related articlesFree article

Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes.

Chou KC.

Bioinformatics. 2005 Jan 1;21(1):10-9. Epub 2004 Aug 12.PMID: 15308540 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparison study on k-word statistical measures for protein: from sequence to 'sequence space'.

Dai Q, Wang T.

BMC Bioinformatics. 2008 Sep 23;9:394.PMID: 18811946 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O.

BMC Bioinformatics. 2008 Jan 11;9:17.PMID: 18190718 [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

Automated functional classification of experimental and predicted protein structures.

Wang K, Samudrala R.

BMC Bioinformatics. 2006 Jun 2;7:278.PMID: 16749925 [PubMed - indexed for MEDLINE]Related articlesFree article

Recognition of protein function using the local similarity.

Alexandrov K, Sobolev B, Filimonov D, Poroikov V.

J Bioinform Comput Biol. 2008 Aug;6(4):709-25.PMID: 18763738 [PubMed - indexed for MEDLINE]Related articles

Automatic annotation of protein function based on family identification.

Abascal F, Valencia A.

Proteins. 2003 Nov 15;53(3):683-92.PMID: 14579359 [PubMed - indexed for MEDLINE]Related articles

Modeling the percolation of annotation errors in a database of protein sequences.

Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA.

Bioinformatics. 2002 Dec;18(12):1641-9.PMID: 12490449 [PubMed - indexed for MEDLINE]Related articlesFree article

FSSA: a novel method for identifying functional signatures from structural alignments.

Wang K, Samudrala R.

Bioinformatics. 2005 Jul 1;21(13):2969-77. Epub 2005 Apr 28.PMID: 15860561 [PubMed - indexed for MEDLINE]Related articlesFree article

A comprehensive system for evaluation of remote sequence similarity detection.

Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV.

BMC Bioinformatics. 2007 Aug 28;8:314.PMID: 17725841 [PubMed - indexed for MEDLINE]Related articlesFree article

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Taly JF, Marin A, Gibrat JF.

BMC Bioinformatics. 2008 Jan 7;9:6.PMID: 18179702 [PubMed - indexed for MEDLINE]Related articlesFree article