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Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.

Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.

Database (Oxford). 2011 Oct 23;2011:bar047. doi: 10.1093/database/bar047. Print 2011.


The Proteomics Identifications database: 2010 update.

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.

Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.


BioMart--biological queries made easy.

Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A.

BMC Genomics. 2009 Jan 14;10:22. doi: 10.1186/1471-2164-10-22.


A guide to the Proteomics Identifications Database proteomics data repository.

Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.

Proteomics. 2009 Sep;9(18):4276-83. doi: 10.1002/pmic.200900402.


Using the PRIDE proteomics identifications database for knowledge discovery and data analysis.

Jones P, Martens L.

Methods Mol Biol. 2010;604:297-307. doi: 10.1007/978-1-60761-444-9_20.


Protein structure as a means to triage proposed PTM sites.

Vandermarliere E, Martens L.

Proteomics. 2013 Mar;13(6):1028-35. doi: 10.1002/pmic.201200232. Epub 2013 Feb 4.


PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Vizcaíno JA, Reisinger F, Côté R, Martens L.

Methods Mol Biol. 2011;696:93-105. doi: 10.1007/978-1-60761-987-1_6.


BioMart Central Portal--unified access to biological data.

Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W23-7. doi: 10.1093/nar/gkp265. Epub 2009 May 6.


PRIDE: new developments and new datasets.

Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.

Nucleic Acids Res. 2008 Jan;36(Database issue):D878-83. Epub 2007 Nov 22.


ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry.

LeDuc RD, Taylor GK, Kim YB, Januszyk TE, Bynum LH, Sola JV, Garavelli JS, Kelleher NL.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W340-5.


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.


Data mining using the Catalogue of Somatic Mutations in Cancer BioMart.

Shepherd R, Forbes SA, Beare D, Bamford S, Cole CG, Ward S, Bindal N, Gunasekaran P, Jia M, Kok CY, Leung K, Menzies A, Butler AP, Teague JW, Campbell PJ, Stratton MR, Futreal PA.

Database (Oxford). 2011 May 23;2011:bar018. doi: 10.1093/database/bar018. Print 2011.


PRIDE: Data submission and analysis.

Vizcaíno JA, Reisinger F, Côté R, Martens L.

Curr Protoc Protein Sci. 2010 Apr;Chapter 25:Unit 25.4. doi: 10.1002/0471140864.ps2504s60.


Integrative cancer genomics (IntOGen) in Biomart.

Perez-Llamas C, Gundem G, Lopez-Bigas N.

Database (Oxford). 2011 Sep 7;2011:bar039. doi: 10.1093/database/bar039. Print 2011.


O-linked N-acetylglucosamine modification of insulin receptor substrate-1 occurs in close proximity to multiple SH2 domain binding motifs.

Klein AL, Berkaw MN, Buse MG, Ball LE.

Mol Cell Proteomics. 2009 Dec;8(12):2733-45. doi: 10.1074/mcp.M900207-MCP200. Epub 2009 Aug 11.


2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2. Erratum in: Nucleic Acids Res. 2016 Dec 15;44(22):11033.


ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry.

Zamdborg L, LeDuc RD, Glowacz KJ, Kim YB, Viswanathan V, Spaulding IT, Early BP, Bluhm EJ, Babai S, Kelleher NL.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W701-6. Epub 2007 Jun 22.


ProSAT2--Protein Structure Annotation Server.

Gabdoulline RR, Ulbrich S, Richter S, Wade RC.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W79-83.

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