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Items: 1 to 20 of 364

1.

Database on Demand - an online tool for the custom generation of FASTA-formatted sequence databases.

Reisinger F, Martens L.

Proteomics. 2009 Sep;9(18):4421-4. doi: 10.1002/pmic.200900254.

PMID:
19725076
2.

Informatics for protein identification by mass spectrometry.

Johnson RS, Davis MT, Taylor JA, Patterson SD.

Methods. 2005 Mar;35(3):223-36. Epub 2005 Jan 13. Review.

PMID:
15722219
3.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2007 Oct 18;8:401.

4.

Proteomics FASTA archive and reference resource.

Falkner JA, Hill JA, Andrews PC.

Proteomics. 2008 May;8(9):1756-7. doi: 10.1002/pmic.200701194.

6.

DBParser: web-based software for shotgun proteomic data analyses.

Yang X, Dondeti V, Dezube R, Maynard DM, Geer LY, Epstein J, Chen X, Markey SP, Kowalak JA.

J Proteome Res. 2004 Sep-Oct;3(5):1002-8.

PMID:
15473689
7.

ProFAT: a web-based tool for the functional annotation of protein sequences.

Bradshaw CR, Surendranath V, Habermann B.

BMC Bioinformatics. 2006 Oct 23;7:466.

9.

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA.

Mol Cell Proteomics. 2007 Sep;6(9):1638-55. Epub 2007 May 27.

10.

Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search.

Dutta D, Chen T.

Bioinformatics. 2007 Mar 1;23(5):612-8. Epub 2007 Jan 19.

PMID:
17237061
11.

OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results.

Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L.

Proteomics. 2009 Jul;9(14):3772-4. doi: 10.1002/pmic.200900037.

PMID:
19639591
12.

Protein structure databases with new web services for structural biology and biomedical research.

Standley DM, Kinjo AR, Kinoshita K, Nakamura H.

Brief Bioinform. 2008 Jul;9(4):276-85. doi: 10.1093/bib/bbn015. Epub 2008 Apr 22. Review.

PMID:
18430752
13.

TOPPView: an open-source viewer for mass spectrometry data.

Sturm M, Kohlbacher O.

J Proteome Res. 2009 Jul;8(7):3760-3. doi: 10.1021/pr900171m.

PMID:
19425593
14.

SysPTM: a systematic resource for proteomic research on post-translational modifications.

Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y.

Mol Cell Proteomics. 2009 Aug;8(8):1839-49. doi: 10.1074/mcp.M900030-MCP200. Epub 2009 Apr 14.

15.

Open source system for analyzing, validating, and storing protein identification data.

Craig R, Cortens JP, Beavis RC.

J Proteome Res. 2004 Nov-Dec;3(6):1234-42.

PMID:
15595733
16.

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.

Yu C, Zavaljevski N, Desai V, Johnson S, Stevens FJ, Reifman J.

BMC Bioinformatics. 2008 Jan 25;9:52. doi: 10.1186/1471-2105-9-52.

17.

CellMontage: similar expression profile search server.

Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P.

Bioinformatics. 2007 Nov 15;23(22):3103-4. Epub 2007 Sep 25. Erratum in: Bioinformatics. 2008 Jun;24(9):1223.

PMID:
17895274
18.

APD: the Antimicrobial Peptide Database.

Wang Z, Wang G.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D590-2.

19.

An algorithm to classify amino acid sequences into protein groups of Bothrops jararacussu venomous gland.

Giuliatti S, Faria M Jr, Camargo F, Camargo LP, Franca SC, Soares AM.

Protein Pept Lett. 2005 May;12(4):333-7.

PMID:
15907177
20.

AgdbNet - antigen sequence database software for bacterial typing.

Jolley KA, Maiden MC.

BMC Bioinformatics. 2006 Jun 21;7:314.

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