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Results: 1 to 20 of 131

1.

PDBML: the representation of archival macromolecular structure data in XML.

Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM.

Bioinformatics. 2005 Apr 1;21(7):988-92. Epub 2004 Oct 27.

PMID:
15509603
[PubMed - indexed for MEDLINE]
Free Article
2.

An extensible automated protein annotation tool: standardizing input and output using validated XML.

Deevi SV, Martin AC.

Bioinformatics. 2006 Feb 1;22(3):291-6. Epub 2005 Dec 8.

PMID:
16339285
[PubMed - indexed for MEDLINE]
Free Article
3.

Using MSDchem to search the PDB ligand dictionary.

Dimitropoulos D, Ionides J, Henrick K.

Curr Protoc Bioinformatics. 2006 Oct;Chapter 14:Unit14.3. doi: 10.1002/0471250953.bi1403s15.

PMID:
18428761
[PubMed - indexed for MEDLINE]
4.

Capturing biological information with class-responsibility-collaboration cards.

Shegogue D, Zheng WJ.

Bioinformatics. 2005 Feb 1;21(3):415-7. Epub 2004 Sep 7.

PMID:
15353449
[PubMed - indexed for MEDLINE]
Free Article
5.

TargetDB: a target registration database for structural genomics projects.

Chen L, Oughtred R, Berman HM, Westbrook J.

Bioinformatics. 2004 Nov 1;20(16):2860-2. Epub 2004 May 6.

PMID:
15130928
[PubMed - indexed for MEDLINE]
Free Article
6.

Pedro: a configurable data entry tool for XML.

Garwood KL, Taylor CF, Runte KJ, Brass A, Oliver SG, Paton NW.

Bioinformatics. 2004 Oct 12;20(15):2463-5. Epub 2004 Apr 8.

PMID:
15073025
[PubMed - indexed for MEDLINE]
Free Article
7.

PDB file parser and structure class implemented in Python.

Hamelryck T, Manderick B.

Bioinformatics. 2003 Nov 22;19(17):2308-10.

PMID:
14630660
[PubMed - indexed for MEDLINE]
Free Article
8.

DisProt: a database of protein disorder.

Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK.

Bioinformatics. 2005 Jan 1;21(1):137-40. Epub 2004 Aug 13.

PMID:
15310560
[PubMed - indexed for MEDLINE]
Free Article
9.

The Protein Data Bank: unifying the archive.

Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne PE, Berman HM.

Nucleic Acids Res. 2002 Jan 1;30(1):245-8.

PMID:
11752306
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.

Fischer D, Paś J, Rychlewski L.

Bioinformatics. 2004 Oct 12;20(15):2482-4. Epub 2004 Apr 8.

PMID:
15073011
[PubMed - indexed for MEDLINE]
Free Article
11.

PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt.

Martin AC.

Bioinformatics. 2004 Apr 12;20(6):986-8. Epub 2004 Feb 5.

PMID:
14764547
[PubMed - indexed for MEDLINE]
Free Article
12.

ProtBuD: a database of biological unit structures of protein families and superfamilies.

Xu Q, Canutescu A, Obradovic Z, Dunbrack RL Jr.

Bioinformatics. 2006 Dec 1;22(23):2876-82. Epub 2006 Oct 2. Erratum in: Bioinformatics. 2007 Aug;23(15):2028.

PMID:
17018535
[PubMed - indexed for MEDLINE]
Free Article
13.

XML for data representation and model specification in neuroscience.

Crook SM, Howell FW.

Methods Mol Biol. 2007;401:53-66. doi: 10.1007/978-1-59745-520-6_4. Review.

PMID:
18368360
[PubMed - indexed for MEDLINE]
14.

CisML: an XML-based format for sequence motif detection software.

Haverty PM, Weng Z.

Bioinformatics. 2004 Jul 22;20(11):1815-7. Epub 2004 Mar 4.

PMID:
15001475
[PubMed - indexed for MEDLINE]
Free Article
15.

Analyzing the simplicial decomposition of spatial protein structures.

Ordög R, Szabadka Z, Grolmusz V.

BMC Bioinformatics. 2008;9 Suppl 1:S11. doi: 10.1186/1471-2105-9-S1-S11.

PMID:
18315842
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

CellML2SBML: conversion of CellML into SBML.

Schilstra MJ, Li L, Matthews J, Finney A, Hucka M, Le Novère N.

Bioinformatics. 2006 Apr 15;22(8):1018-20. Epub 2006 Feb 10.

PMID:
16473867
[PubMed - indexed for MEDLINE]
Free Article
17.

Seq2Struct: a resource for establishing sequence-structure links.

Via A, Zanzoni A, Helmer-Citterich M.

Bioinformatics. 2005 Feb 15;21(4):551-3. Epub 2004 Sep 28.

PMID:
15454411
[PubMed - indexed for MEDLINE]
Free Article
18.

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

Kinjo AR, Yamashita R, Nakamura H.

Database (Oxford). 2010 Aug 25;2010:baq021. doi: 10.1093/database/baq021.

PMID:
20798081
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Domain-based small molecule binding site annotation.

Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW.

BMC Bioinformatics. 2006 Mar 17;7:152.

PMID:
16545112
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A systematic approach to modeling, capturing, and disseminating proteomics experimental data.

Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR 3rd, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG.

Nat Biotechnol. 2003 Mar;21(3):247-54.

PMID:
12610571
[PubMed - indexed for MEDLINE]

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