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Results: 1 to 20 of 69

1.

Protein domain analysis in the era of complete genomes.

Copley RR, Doerks T, Letunic I, Bork P.

FEBS Lett. 2002 Feb 20;513(1):129-34. Review.

PMID:
11911892
[PubMed - indexed for MEDLINE]
Free Article
2.

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]
3.

ProtRepeatsDB: a database of amino acid repeats in genomes.

Kalita MK, Ramasamy G, Duraisamy S, Chauhan VS, Gupta D.

BMC Bioinformatics. 2006 Jul 7;7:336.

PMID:
16827924
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

FASSM: enhanced function association in whole genome analysis using sequence and structural motifs.

Gaurav K, Gupta N, Sowdhamini R.

In Silico Biol. 2005;5(5-6):425-38.

PMID:
16268788
[PubMed - indexed for MEDLINE]
5.
6.

The PAS fold. A redefinition of the PAS domain based upon structural prediction.

Hefti MH, Fran├žoijs KJ, de Vries SC, Dixon R, Vervoort J.

Eur J Biochem. 2004 Mar;271(6):1198-208.

PMID:
15009198
[PubMed - indexed for MEDLINE]
7.

GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures.

Yabuki Y, Mukai Y, Swindells MB, Suwa M.

Bioinformatics. 2004 Mar 1;20(4):596-8. Epub 2004 Jan 29.

PMID:
14751990
[PubMed - indexed for MEDLINE]
Free Article
8.

Amino acid recognition by Venus flytrap domains is encoded in an 8-residue motif.

Acher FC, Bertrand HO.

Biopolymers. 2005;80(2-3):357-66.

PMID:
15810013
[PubMed - indexed for MEDLINE]
9.

The SUPERFAMILY database in structural genomics.

Gough J.

Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1897-900. Epub 2002 Oct 21. Review.

PMID:
12393919
[PubMed - indexed for MEDLINE]
10.

N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence.

Maurer-Stroh S, Eisenhaber B, Eisenhaber F.

J Mol Biol. 2002 Apr 5;317(4):541-57.

PMID:
11955008
[PubMed - indexed for MEDLINE]
11.

Identification and distribution of protein families in 120 completed genomes using Gene3D.

Lee D, Grant A, Marsden RL, Orengo C.

Proteins. 2005 May 15;59(3):603-15.

PMID:
15768405
[PubMed - indexed for MEDLINE]
12.

Applications of InterPro in protein annotation and genome analysis.

Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.

Brief Bioinform. 2002 Sep;3(3):285-95.

PMID:
12230037
[PubMed - indexed for MEDLINE]
Free Article
13.

Protein functional annotation by homology.

Mazumder R, Vasudevan S, Nikolskaya AN.

Methods Mol Biol. 2008;484:465-90. doi: 10.1007/978-1-59745-398-1_28.

PMID:
18592196
[PubMed - indexed for MEDLINE]
14.

Genome bias influences amino acid choices: analysis of amino acid substitution and re-compilation of substitution matrices exclusive to an AT-biased genome.

Paila U, Kondam R, Ranjan A.

Nucleic Acids Res. 2008 Dec;36(21):6664-75. doi: 10.1093/nar/gkn635. Epub 2008 Oct 23.

PMID:
18948281
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

SMART 4.0: towards genomic data integration.

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D142-4.

PMID:
14681379
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes.

Cummings L, Riley L, Black L, Souvorov A, Resenchuk S, Dondoshansky I, Tatusova T.

FEMS Microbiol Lett. 2002 Nov 5;216(2):133-8.

PMID:
12435493
[PubMed - indexed for MEDLINE]
17.

On the detection of functionally coherent groups of protein domains with an extension to protein annotation.

McLaughlin WA, Chen K, Hou T, Wang W.

BMC Bioinformatics. 2007 Oct 16;8:390.

PMID:
17937820
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Predicting protein function from domain content.

Forslund K, Sonnhammer EL.

Bioinformatics. 2008 Aug 1;24(15):1681-7. doi: 10.1093/bioinformatics/btn312. Epub 2008 Jun 30. Erratum in: Bioinformatics. 2009 May 1;25(9):1214.

PMID:
18591194
[PubMed - indexed for MEDLINE]
Free Article
19.

The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis.

Bartoli L, Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G, Maggi GP, Casadio R.

J Proteome Res. 2009 Sep;8(9):4362-71. doi: 10.1021/pr900204r.

PMID:
19552451
[PubMed - indexed for MEDLINE]
20.

ELISA: a unified, multidimensional view of the protein domain universe.

Shakhnovich BE, Harvey JM, Delisi C.

Genome Inform. 2004;15(1):213-20.

PMID:
15712123
[PubMed - indexed for MEDLINE]

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