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Items: 1 to 20 of 115

1.

Framework for a protein ontology.

Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH.

BMC Bioinformatics. 2007 Nov 27;8 Suppl 9:S1.

2.

TGF-beta signaling proteins and the Protein Ontology.

Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S3. doi: 10.1186/1471-2105-10-S5-S3.

3.

A tutorial on protein ontology resources for proteomic studies.

Arighi CN.

Methods Mol Biol. 2011;694:77-90. doi: 10.1007/978-1-60761-977-2_6.

4.

GoFigure: automated Gene Ontology annotation.

Khan S, Situ G, Decker K, Schmidt CJ.

Bioinformatics. 2003 Dec 12;19(18):2484-5.

PMID:
14668239
5.

IPPRED: server for proteins interactions inference.

Goffard N, Garcia V, Iragne F, Groppi A, de Daruvar A.

Bioinformatics. 2003 May 1;19(7):903-4.

PMID:
12724307
7.

GOChase: correcting errors from Gene Ontology-based annotations for gene products.

Park YR, Park CH, Kim JH.

Bioinformatics. 2005 Mar;21(6):829-31. Epub 2004 Oct 28.

PMID:
15513987
8.

Using the blocks database to recognize functional domains.

Henikoff JG, Greene EA, Taylor N, Henikoff S, Pietrokovski S.

Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.2. doi: 10.1002/0471250953.bi0202s00.

PMID:
18792933
9.

Web-based interface facilitating sequence-to-structure analysis of BLAST alignment reports.

Ganesan N, Bennett NF, Velauthapillai M, Pattabiraman N, Squier R, Kalyanasundaram B.

Biotechniques. 2005 Aug;39(2):186, 188. No abstract available.

10.

DWARF--a data warehouse system for analyzing protein families.

Fischer M, Thai QK, Grieb M, Pleiss J.

BMC Bioinformatics. 2006 Nov 9;7:495.

11.

OBO Explorer: an editor for Open Biomedical Ontologies in OWL.

Aitken S, Chen Y, Bard J.

Bioinformatics. 2008 Feb 1;24(3):443-4. Epub 2007 Dec 1.

PMID:
18056066
12.

A top-level ontology of functions and its application in the Open Biomedical Ontologies.

Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H, Kelso J.

Bioinformatics. 2006 Jul 15;22(14):e66-73.

PMID:
16873523
13.

The Gene Ontology in 2010: extensions and refinements.

Gene Ontology Consortium..

Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. Epub 2009 Nov 17.

14.

MPSS: an integrated database system for surveying a set of proteins.

Hao P, He WZ, Huang Y, Ma LX, Xu Y, Xi H, Wang C, Liu BS, Wang JM, Li YX, Zhong Y.

Bioinformatics. 2005 May 1;21(9):2142-3. Epub 2005 Feb 4.

PMID:
15699026
15.

GeneTools--application for functional annotation and statistical hypothesis testing.

Beisvag V, Jünge FK, Bergum H, Jølsum L, Lydersen S, Günther CC, Ramampiaro H, Langaas M, Sandvik AK, Laegreid A.

BMC Bioinformatics. 2006 Oct 24;7:470.

16.

CoC: a database of universally conserved residues in protein folds.

Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA.

Bioinformatics. 2005 May 15;21(10):2539-40. Epub 2005 Mar 3.

PMID:
15746286
17.

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.

18.

The Protein Ontology: a structured representation of protein forms and complexes.

Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D539-45. doi: 10.1093/nar/gkq907. Epub 2010 Oct 8.

19.

The InterPro database and tools for protein domain analysis.

Mulder NJ, Apweiler R.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 2:Unit 2.7. doi: 10.1002/0471250953.bi0207s21.

PMID:
18428686
20.

OBO to OWL: a protege OWL tab to read/save OBO ontologies.

Moreira DA, Musen MA.

Bioinformatics. 2007 Jul 15;23(14):1868-70. Epub 2007 May 12.

PMID:
17496317

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