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Protein Bioinformatics Databases and Resources

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Book cover Protein Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1558))

Abstract

Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.

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References

  1. Ridley M (2006) Genome. Harper Perennial, New York

    Google Scholar 

  2. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW (1997) Characterization of the yeast transcriptome. Cell 2:243–251

    Article  Google Scholar 

  3. Anderson NL, Anderson NG (1998) Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 11:1853–1861

    Article  Google Scholar 

  4. Hye A, Lynham S, Thambisetty M, Causevic M, Campbell J, Byers HL, Hooper C, Rijsdijk F, Tabrizi SJ, Banner S, Shaw CE, Foy C, Poppe M, Archer N, Hamilton G, Powell J, Brown RG, Sham P, Ward M, Lovestone S (2006) Proteome-based plasma biomarkers for Alzheimer’s disease. Brain 11:3042–3050

    Article  Google Scholar 

  5. Decramer S, Wittke S, Mischak H, Zürbig P, Walden M, Bouissou F, Bascands JL, Schanstra JP (2006) Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis. Nat Med 4:398–400

    Article  CAS  Google Scholar 

  6. Metzker M (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  7. Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, Wu CH (2011) A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics 27:1190–1191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Chen C, Huang H, Wu CH (2011) Protein bioinformatics databases and resources. Methods Mol Biol 694:3–24

    Article  PubMed  CAS  Google Scholar 

  9. Farrell CM, O’Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD (2014) Current status and new features of the consensus coding sequence database. Nucleic Acids Res 42:D865–D872

    Article  CAS  PubMed  Google Scholar 

  10. Kodama Y, Mashima J, Kosuge T, Katayama T, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y (2015) The DDBJ Japanese genotype-phenotype archive for genetic and phenotypic human data. Nucleic Acids Res 43:D18–D22

    Article  PubMed  Google Scholar 

  11. Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R (2007) EMBL nucleotide sequence database in 2006. Nucleic Acids Res 35:D16–D20

    Article  CAS  PubMed  Google Scholar 

  12. Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, Bourexis D, Brister J, Bryant SH, Canese K, Clark K, DiCuccio M, Dondoshansky I, Federhen S, Feolo M, Funk K, Geer LY, Gorelenkov V, Hoeppner M, Holmes B, Johnson M, Khotomlianski V, Kimchi A, Kimelman M, Kitts P, Klimke W, Krasnov S, Kuznetsov A, Landrum MJ, Landsman D, Lee JM, Lipman DJ, Lu Z, Madden TL, Madej T, Marchler-Bauer A, Karsch-Mizrachi I, Murphy T, Orris R, Ostell J, O’Sullivan C, Panchenko A, Phan L, Preuss D, Pruitt KD, Rubinstein W, Sayers EW, Schneider V, Schuler GD, Sherry ST, Sirotkin K, Siyan K, Slotta D, Soboleva A, Soussov V, Starchenko G, Tatusova TA, Trawick BW, Vakatov D, Wang Y, Ward M, Wilbur W, Yaschenko E, Zbicz K (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 43:D6–D17

    Article  Google Scholar 

  13. Pruitt KD, Tatusova T, Maglott DR (2006) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61–D65

    Article  PubMed  PubMed Central  Google Scholar 

  14. The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212

    Article  Google Scholar 

  15. Pitarch A, Sánchez M, Nombela C, Gil C (2003) Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002). J Chromatogr B Analyt Technol Biomed Life Sci 787:129–148

    Article  CAS  PubMed  Google Scholar 

  16. Zhou T, Zhou ZM, Guo XJ (2013) Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. Asian J Androl 15:594–602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hoogland C, Mostaguir K, Sanchez JC, Hochstrasser DF, Appel RD (2004) SWISS-2DPAGE, ten years later. Proteomics 4:2352–2356

    Article  CAS  PubMed  Google Scholar 

  18. Hoogland C, Mostaguir K, Appel RD, Lisacek F (2008) The World-2DPAGE constellation to promote and publish gel-based proteomics data through the ExPASy server. J Proteomics 71:245–248

    Article  CAS  PubMed  Google Scholar 

  19. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK (2007) DisProt: the database of disordered proteins. Nucleic Acids Res 35:D786–D793

    Article  CAS  PubMed  Google Scholar 

  20. Potenza E, Di Domenico T, Walsh I, Tosatto SC (2014) MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic Acids Res 43:D315–D320

    Article  PubMed  PubMed Central  Google Scholar 

  21. Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A (2014) ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 42:D336–D346

    Article  CAS  PubMed  Google Scholar 

  22. Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert TJ, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ (2015) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res 44:D385–D395

    Google Scholar 

  23. Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H (2012) Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 40:D453–D460

    Article  CAS  PubMed  Google Scholar 

  24. de Beer TA, Berka K, Thornton JM, Laskowski RA (2014) PDBsum additions. Nucleic Acids Res 42:D292–D296

    Article  PubMed  CAS  Google Scholar 

  25. Haas J, Roth S, Arnold K, Kiefer F, Schmidt T, Bordoli L, Schwede T (2013) The protein model portal-a comprehensive resource for protein structure and model information. Database. doi:10.1093/database/bat031

    PubMed  PubMed Central  Google Scholar 

  26. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381–3385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35:D198–D201

    Article  CAS  PubMed  Google Scholar 

  29. Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Res 42:D1083–D1090

    Article  CAS  PubMed  Google Scholar 

  30. Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y, Maciejewski A, Arndt D, Wilson M, Neveu V, Tang A, Gabriel G, Ly C, Adamjee S, Dame ZT, Han B, Zhou Y, Wishart DS (2014) DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res 42:D1091–D1097

    Article  CAS  PubMed  Google Scholar 

  31. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 42:D459–D471

    Article  CAS  PubMed  Google Scholar 

  32. Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D (2015) BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res 43:D439–D446

    Article  PubMed  Google Scholar 

  33. Bairoch A (2000) The ENZYME database in 2000. Nucleic Acids Res 28:304–305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D’Eustachio P (2014) The reactome pathway knowledgebase. Nucleic Acids Res 42:D472–D477

    Article  CAS  PubMed  Google Scholar 

  35. Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Müller W (2012) SABIO-RK—database for biochemical reaction kinetics. Nucleic Acids Res 40:D790–D796

    Article  CAS  PubMed  Google Scholar 

  36. Fazekas D, Koltai M, Türei D, Módos D, Pálfy M, Dúl Z, Zsákai L, Szalay-Bekő M, Lenti K, Farkas IJ, Vellai T, Csermely P, Korcsmáros T (2013) SignaLink 2—a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol 7:7

    Article  PubMed  PubMed Central  Google Scholar 

  37. Morgat A, Coissac E, Coudert E, Axelsen KB, Keller G, Bairoch A, Bridge A, Bougueleret L, Xenarios I, Viari A (2012) UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res 40:D761–D769

    Article  CAS  PubMed  Google Scholar 

  38. Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA (2006) Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res 34:D281–D284

    Article  CAS  PubMed  Google Scholar 

  39. Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A (2015) HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res 43:D1064–D1070

    Article  PubMed  Google Scholar 

  40. Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD (2015) The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 43:D213–D221

    Article  PubMed  Google Scholar 

  41. Mi H, Muruganujan A, Casagrande JT, Thomas PD (2013) Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 8:1551–1566

    Article  PubMed  CAS  Google Scholar 

  42. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014) The Pfam protein families database. Nucleic Acids Res 42:D222–D230

    Article  CAS  PubMed  Google Scholar 

  43. Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res 32:D112–D114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, Mitchell A, Moulton G, Nordle A, Paine K, Taylor P, Uddin A, Zygouri C (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res 31:400–402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Servant F, Bru C, Carrère S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002) ProDom: Automated clustering of homologous domains. Brief Bioinform 3:246–251

    Article  CAS  PubMed  Google Scholar 

  46. Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I (2013) New and continuing developments at PROSITE. Nucleic Acids Res 41:D344–D347

    Article  CAS  PubMed  Google Scholar 

  47. Rappoport N, Karsenty S, Stern A, Linial N, Linial M (2011) ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. Nucleic Acids Res 40:D313–D320

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Letunic I, Doerks T, Bork P (2015) SMART: recent updates, new developments and status in 2015. Nucleic Acids Res 43:D257–D260

    Article  PubMed  Google Scholar 

  49. Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J (2009) SUPERFAMILY—comparative genomics, datamining and sophisticated visualisation. Nucleic Acids Res 37:D380–D386

    Article  CAS  PubMed  Google Scholar 

  50. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O (2007) TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35:D260–D264

    Article  CAS  PubMed  Google Scholar 

  51. Bastian F, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M (2008) Bgee: integrating and comparing heterogeneous transcriptome data among species. Lect Notes Comput Sci 5109:124–131

    Article  CAS  Google Scholar 

  52. Praz V, Jagannathan V, Bucher P (2004) CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res 32:D542–D547

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Grennan AK (2006) Genevestigator. Facilitating web-based gene-expression analysis. Plant Physiol 141:1164–1166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A (2014) Expression atlas update-a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res 42:D926–D932

    Article  CAS  PubMed  Google Scholar 

  55. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P (2015) Ensembl 2015. Nucleic Acids Res 43:D662–D669

    Article  PubMed  Google Scholar 

  56. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A (2010) Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res 38:D563–D569

    Article  CAS  PubMed  Google Scholar 

  57. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 33:D54–D58

    Article  CAS  PubMed  Google Scholar 

  58. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2015) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D462

    Google Scholar 

  59. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591

    Article  CAS  PubMed  Google Scholar 

  60. Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ (2015) The UCSC genome browser database: 2015 update. Nucleic Acids Res 43:D670–D681

    Article  PubMed  Google Scholar 

  61. Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Emmert D, Hammond M, Hill CA, Kennedy RC, Lobo NF, MacCallum MR, Madey G, Megy K, Redmond S, Russo S, Severson DW, Stinson EO, Topalis P, Zdobnov EM, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH (2007) VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res 35:D503–D505

    Article  CAS  PubMed  Google Scholar 

  62. Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW (2014) WormBase 2014: new views of curated biology. Nucleic Acids Res 42:D789–D793

    Article  CAS  PubMed  Google Scholar 

  63. Herzig V, Wood DL, Newell F, Chaumeil PA, Kaas Q, Binford GJ, Nicholson GM, Gorse D, King GF (2011) ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. Nucleic Acids Res 39:D653–D657

    Article  CAS  PubMed  Google Scholar 

  64. Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G (2012) The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res 40:D667–D674

    Article  CAS  PubMed  Google Scholar 

  65. Kaas Q, Yu R, Jin AH, Dutertre S, Craik DJ (2012) ConoServer: updated content, knowledge, and discovery tools in the conopeptide database. Nucleic Acids Res 40:D325–D330

    Article  CAS  PubMed  Google Scholar 

  66. Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ (2015) The comparative toxicogenomics database’s 10th year anniversary: update 2015. Nucleic Acids Res 43:D914–D920

    Article  PubMed  Google Scholar 

  67. Basu S, Fey P, Pandit Y, Dodson RJ, Kibbe WA, Chisholm RL (2013) DictyBase 2013: integrating multiple Dictyostelid species. Nucleic Acids Res 41:D676–D683

    Article  CAS  PubMed  Google Scholar 

  68. Misra RV, Horler RS, Reindl W, Goryanin II, Thomas GH (2005) EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res 33:D329–D333

    Article  CAS  PubMed  Google Scholar 

  69. Zhou J, Rudd KE (2013) EcoGene 3.0. Nucleic Acids Res 41:D613–D624

    Article  CAS  PubMed  Google Scholar 

  70. Combet C, Garnier N, Charavay C, Grando D, Crisan D, Lopez J, Dehne-Garcia A, Geourjon C, Bettler E, Hulo C, Mercier PL, Bartenschlager R, Diepolder H, Moradpour D, Pawlotsky JM, Rice CM, Trepo C, Penin F, Deléage G (2007) euHCVdb: the European hepatitis C virus database. Nucleic Acids Res 35:D363–D366

    Article  CAS  PubMed  Google Scholar 

  71. Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res 38:D415–D419

    Article  CAS  PubMed  Google Scholar 

  72. dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM, FlyBase Consortium (2015) FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res 43:D690–D697

    Article  PubMed  Google Scholar 

  73. Frézal J (1998) Genatlas database, genes and development defects. C R Acad Sci III 321:805–817

    Article  PubMed  Google Scholar 

  74. Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, Olender T, Chalifa-Caspi V, Lancet D (2002) GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18:1542–1543

    Article  CAS  PubMed  Google Scholar 

  75. Lechat P, Hummel L, Rousseau S, Moszer I (2008) GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res 36:D469–D474

    Article  CAS  PubMed  Google Scholar 

  76. Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D’Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 42:D1193–D1199

    Article  CAS  PubMed  Google Scholar 

  77. Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, Imanishi T, Gojobori T (2009) H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res 38:D626–D632

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA (2013) Genenames.org: the HGNC resources in 2013. Nucleic Acids Res 41:D545–D552

    Article  CAS  PubMed  Google Scholar 

  79. Uhlén M, Björling E, Agaton C, Szigyarto CA, Amini B, Andersen E, Andersson AC, Angelidou P, Asplund A, Asplund C, Berglund L, Bergström K, Brumer H, Cerjan D, Ekström M, Elobeid A, Eriksson C, Fagerberg L, Falk R, Fall J, Forsberg M, Björklund MG, Gumbel K, Halimi A, Hallin I, Hamsten C, Hansson M, Hedhammar M, Hercules G, Kampf C, Larsson K, Lindskog M, Lodewyckx W, Lund J, Lundeberg J, Magnusson K, Malm E, Nilsson P, Odling J, Oksvold P, Olsson I, Oster E, Ottosson J, Paavilainen L, Persson A, Rimini R, Rockberg J, Runeson M, Sivertsson A, Sköllermo A, Steen J, Stenvall M, Sterky F, Strömberg S, Sundberg M, Tegel H, Tourle S, Wahlund E, Waldén A, Wan J, Wernérus H, Westberg J, Wester K, Wrethagen U, Xu LL, Hober S, Pontén F (2005) A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 4:1920–1932

    Article  PubMed  CAS  Google Scholar 

  80. Kikuno R, Nagase T, Nakayama M, Koga H, Okazaki N, Nakajima D, Ohara O (2004) HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE. Nucleic Acids Res 32:D502–D504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Moszer I, Glaser P, Danchin A (1995) SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141:261–268

    Article  CAS  PubMed  Google Scholar 

  82. Kapopoulou A, Lew JM, Cole ST (2011) The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes. Tuberculosis (Edinb) 91:8–13

    Article  CAS  Google Scholar 

  83. Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Richter JD, Sen TZ, Lawrence CJ (2015) MaizeGDB 2015: New tools, data, and interface for the maize model organism database. Nucleic Acids Res 44:D1195–D1201

    Google Scholar 

  84. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, The Mouse Genome Database Group (2015) The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res 43:D726–D736

    Article  PubMed  Google Scholar 

  85. Biaudet V, Samson F, Bessières P (1997) Micado-a network-oriented database for microbial genomes. Comput Appl Biosci 13:431–438

    CAS  PubMed  Google Scholar 

  86. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514–D517

    Article  CAS  PubMed  Google Scholar 

  87. Gaudet P, Argoud-Puy G, Cusin I, Duek P, Evalet O, Gateau A, Gleizes A, Pereira M, Zahn-Zabal M, Zwahlen C, Bairoch A, Lane L (2013) neXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res 12:293–298

    Article  CAS  PubMed  Google Scholar 

  88. Aymé S, Schmidtke J (2007) Networking for rare diseases: a necessity for Europe. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 50:1477–1483

    Article  PubMed  Google Scholar 

  89. Thorn CF, Klein TE, Altman RB (2005) PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol 311:179–191

    CAS  PubMed  Google Scholar 

  90. Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG (2012) PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res 40:D695–D699

    Article  CAS  PubMed  Google Scholar 

  91. Winsor GL, Lo R, Ho Sui SJ, Ung KS, Huang S, Cheng D, Ching WK, Hancock RE, Brinkman FS (2005) Pseudomonas aeruginosa genome database and pseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res 33:D338–D343

    Article  CAS  PubMed  Google Scholar 

  92. Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H (2015) The rat genome database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res 28:D743–D750

    Article  Google Scholar 

  93. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res 40:D700–D705

    Article  CAS  PubMed  Google Scholar 

  94. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210

    Article  CAS  PubMed  Google Scholar 

  95. Lew JM, Kapopoulou A, Jones LM, Cole ST (2011) TubercuList—10 years after. Tuberculosis (Edinb) 1:1–7

    Article  Google Scholar 

  96. Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD (2008) Xenbase: a Xenopus biology and genomics resource. Nucleic Acids Res 36:D761–D767

    Article  CAS  PubMed  Google Scholar 

  97. Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M (2013) ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res 41:D854–D860

    Article  CAS  PubMed  Google Scholar 

  98. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 42:D231–D239

    Article  CAS  PubMed  Google Scholar 

  99. Perrière G, Duret L, Gouy M (2000) HOBACGEN: database system for comparative genomics in bacteria. Genome Res 10:379–385

    Article  PubMed  PubMed Central  Google Scholar 

  100. Duret L, Mouchiroud D, Gouy M (1994) HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res 22:2360–2365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Sonnhammer EL, Östlund G (2015) InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res 43:D234–D239

    Article  PubMed  Google Scholar 

  102. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C (2015) The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 43:D240–D249

    Article  PubMed  Google Scholar 

  104. Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res 41:D358–D365

    Article  CAS  PubMed  Google Scholar 

  105. Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T (2014) PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res 42:D897–D902

    Article  CAS  PubMed  Google Scholar 

  106. Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R (2008) TreeFam: 2008 update. Nucleic Acids Res 36:D735–D740

    Article  CAS  PubMed  Google Scholar 

  107. Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R (2014) A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). Database. doi:10.1093/database/bau022

  108. Peterson TA, Adadey A, Santana-Cruz I, Sun Y, Winder A, Kann MG (2010) DMDM: Domain Mapping of Disease Mutations. Bioinformatics 26:2458–2459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O’Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M (2015) The BioGRID interaction database: 2015 update. Nucleic Acids Res 43:D470–D478

    Article  PubMed  Google Scholar 

  110. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32:D449–D451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H (2014) The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42:D358–D363

    Article  CAS  PubMed  Google Scholar 

  112. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40:D857–D861

    Article  CAS  PubMed  Google Scholar 

  113. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452

    Article  PubMed  Google Scholar 

  114. Schaab C, Geiger T, Stoehr G, Cox J, Mann M (2012) Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol Cell Proteomics 11:M111.014068

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  115. Wang M, Herrmann CJ, Simonovic M, Szklarczyk D, von Mering C (2015) Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics 15:3163–3168

    Article  CAS  PubMed  Google Scholar 

  116. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R (2006) The PeptideAtlas project. Nucleic Acids Res 34:D655–D658

    Article  CAS  PubMed  Google Scholar 

  117. Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O’Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Rios D, Wang R, Hermjakob H (2013) The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 41:D1063–D1069

    Article  CAS  PubMed  Google Scholar 

  118. Wienkoop S, Staudinger C, Hoehenwarter W, Weckwerth W, Egelhofer V (2012) ProMEX—a mass spectral reference database for plant proteomics. Front Plant Sci 3:125

    Article  PubMed  PubMed Central  Google Scholar 

  119. Duan G, Li X, Köhn M (2015) The human DEPhOsphorylation database DEPOD: a 2015 update. Nucleic Acids Res 43:D531–D535

    Article  PubMed  Google Scholar 

  120. Ross KE, Arighi CN, Ren J, Huang H, Wu CH (2013) Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. Database doi:10.1093/database/bat038

  121. Durek P, Schmidt R, Heazlewood JL, Jones A, Maclean D, Nagel A, Kersten B, Schulze WX (2010) PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res 38:D828–D834

    Article  CAS  PubMed  Google Scholar 

  122. Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res 39:D261–DD27

    Article  CAS  PubMed  Google Scholar 

  123. Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Tyers M (2013) The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. Database doi:10.1093/database/bat026

  124. Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E (2014) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 43:D512–D520

    Article  PubMed  PubMed Central  Google Scholar 

  125. Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH (2014) UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res 42:D215–D221

    Article  CAS  PubMed  Google Scholar 

  126. The Gene Ontology Consortium (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res 43:D1049–D1056

    Article  Google Scholar 

  127. Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D’Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH (2014) Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res 42:D415–D421

    Article  CAS  PubMed  Google Scholar 

  128. Mari A, Rasi C, Palazzo P, Scala E (2009) Allergen databases: current status and perspectives. Curr Allergy Asthma Rep 9:376–383

    Article  PubMed  Google Scholar 

  129. Lombard V, Golaconda RH, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495

    Article  CAS  PubMed  Google Scholar 

  130. Lenfant N, Hotelier T, Velluet E, Bourne Y, Marchot P, Chatonnet A (2013) ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins: tools to explore diversity of functions. Nucleic Acids Res 41:D423–D429

    Article  CAS  PubMed  Google Scholar 

  131. Isberg V, Vroling B, van der Kant R, Li K, Vriend G, Gloriam D (2014) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res 42:D422–D425

    Article  CAS  PubMed  Google Scholar 

  132. Giudicelli V, Duroux P, Ginestoux C, Folch G, Jabado-Michaloud J, Chaume D, Lefranc MP (2006) IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res 34:D781–D784

    Article  CAS  PubMed  Google Scholar 

  133. Rawlings ND, Waller M, Barrett AJ, Bateman A (2014) MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 42:D503–D509

    Article  CAS  PubMed  Google Scholar 

  134. Jeffery CJ (1999) Moonlighting proteins. Trends Biochem Sci 24:8–11

    Article  CAS  PubMed  Google Scholar 

  135. Murphy C, Powlowski J, Wu M, Butler G, Tsang A (2011) Curation of characterized glycoside hydrolases of fungal origin. Database. doi:10.1093/database/bar020

    Google Scholar 

  136. Fawal N, Li Q, Savelli B, Brette M, Passaia G, Fabre M, Mathé C, Dunand C (2013) PeroxiBase: a database for large-scale evolutionary analysis of peroxidases. Nucleic Acids Res 41:D441–D414

    Article  CAS  PubMed  Google Scholar 

  137. Roberts RJ, Vincze T, Posfai J, Macelis D (2015) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 43:D298–D299

    Article  PubMed  Google Scholar 

  138. Saier MH, Reddy VS, Tamang DG, Vastermark A (2014) The transporter classification database. Nucleic Acids Res 42:D251–D258

    Article  CAS  PubMed  Google Scholar 

  139. Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres LE, Ben-Hur A, Valencia A (2013) ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res 41:D142–D151

    Article  CAS  PubMed  Google Scholar 

  140. Mihalek I, Res I, Lichtarge O (2004) A family of evolution-entropy hybrid methods for ranking of protein residues by importance. J Mol Biol 336:1265–1282

    Article  CAS  PubMed  Google Scholar 

  141. Good BM, Clarke EL, de Alfaro L, Su AI (2012) The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res 40:D1255–D1261

    Article  CAS  PubMed  Google Scholar 

  142. Schmidt EE, Pelz O, Buhlmann S, Kerr G, Horn T, Boutros M (2013) GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res 41:D1021–D1026

    Article  CAS  PubMed  Google Scholar 

  143. Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM (2009) PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res 37:D611–D618

    Article  CAS  PubMed  Google Scholar 

  144. Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA (2003) SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res 31:219–223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010. https://www.ncbi.nlm.nih.gov/books/NBK25501/

  146. Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R (2004) UniProt archive. Bioinformatics 20:3236–3237

    Article  CAS  PubMed  Google Scholar 

  147. Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, UniProt Consortium (2015) UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31:926–932

    Article  CAS  PubMed  Google Scholar 

  148. Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R (2011) Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One 6:e18910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Mostaguir K, Hoogland C, Binz PA, Appel RD (2003) The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases. Proteomics 3:1441–1444

    Article  CAS  PubMed  Google Scholar 

  150. Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10:980

    Article  CAS  PubMed  Google Scholar 

  151. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent WR, Yao H, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408

    Article  CAS  PubMed  Google Scholar 

  152. Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM (2005) PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21:988–992

    Article  CAS  PubMed  Google Scholar 

  153. Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010) Pathway tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 11:40–79

    Article  CAS  PubMed  Google Scholar 

  154. Dale JM, Popescu L, Karp PD (2010) Machine learning methods for metabolic pathway prediction. BMC Bioinformatics 11:15

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  155. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res 43:W589–W598

    Article  PubMed  PubMed Central  Google Scholar 

  157. De Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34:W362–W365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A (2015) ArrayExpress update-simplifying data submissions. Nucleic Acids Res 43:D1113–D1116

    Article  PubMed  Google Scholar 

  159. Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ (2015) Navigating protected genomics data with UCSC Genome Browser in a Box. Bioinformatics 31:764–766

    Article  CAS  PubMed  Google Scholar 

  160. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH (2009) JBrowse: a next-generation genome browser. Genome Res 19:630–638

    Article  CAS  Google Scholar 

  161. Adler BT, de Alfaro L, Kulshreshtha A, Pye I (2011) Reputation systems for open collaboration. Commun ACM 54:81–87

    PubMed  PubMed Central  Google Scholar 

  162. Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 9:345–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 25:894–898

    Article  CAS  PubMed  Google Scholar 

  164. Hermjakob H (2006) The HUPO proteomics standards initiative—overcoming the fragmentation of proteomics data. Proteomics 6:34–38

    Article  PubMed  CAS  Google Scholar 

  165. Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41:D456–D463

    Article  CAS  PubMed  Google Scholar 

  166. Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22:1459–1466

    Article  CAS  PubMed  Google Scholar 

  167. Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5:976–989

    Article  CAS  PubMed  Google Scholar 

  168. Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74:5383–5392

    Article  CAS  PubMed  Google Scholar 

  169. Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75:4646–4658

    Article  CAS  PubMed  Google Scholar 

  170. Wein SP, Cote RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaino JA (2012) Improvements in the protein identifier cross-reference service. Nucleic Acids Res 40:W276–W280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Cote R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H (2010) The ontology lookup service: bigger and better. Nucleic Acids Res 38:W155–W160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Reisinger F, Martens L (2009) Database on demand—an online tool for the custom generation of FASTA formatted sequence databases. Proteomics 9:4421–4424

    Article  CAS  PubMed  Google Scholar 

  173. Hermjakob H, Apweiler R (2006) The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev Proteomics 3:1–3

    Article  PubMed  Google Scholar 

  174. Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti R, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R (2004) A common open representation of mass spectrometry data and its application in a proteomics research environment. Nat Biotechnol 22:1459–1466

    Article  CAS  PubMed  Google Scholar 

  175. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A (2009) Human protein reference database-2009 update. Nucleic Acids Res 37:D767–D772

    Article  CAS  PubMed  Google Scholar 

  176. Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O’Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 8:528–529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Torii M, Arighi CN, Li G, Wang Q, Wu CH, Vijay-Shanker K (2015) RLIMS-P 2.0: a generalizable rule-based information extraction system for literature mining of protein phosphorylation information. IEEE/ACM Trans Comput Biol Bioinform 12:17–29

    Article  PubMed  PubMed Central  Google Scholar 

  178. Tudor CO, Ross KE, Li G, Vijay-Shanker K, Wu CH, Arighi CN (2015) Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database doi:10.1093/database/bav020

  179. Cooper CA, Harrison MJ, Wilkins MR, Packer NH (2001) GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res 29:332–335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM (2011) EUROCarbDB: an open-access platform for glycoinformatics. Glycobiology 21:493–502

    Article  PubMed  CAS  Google Scholar 

  181. Campbell MP, Royle L, Radcliffe CM, Dwek RA, Rudd PM (2008) GlycoBase and autoGU: tools for HPLC-based glycan analysis. Bioinformatics 24:1214–1216

    Article  CAS  PubMed  Google Scholar 

  182. The OpenSFS and Lustre Community Portal. http://lustre.opensfs.org

  183. The Apache Hadoop Project. http://hadoop.apache.org

  184. The Apache Hive data warehouse software. http://hive.apache.org

  185. The Apache Pig platform. http://pig.apache.org

  186. The Apache Spark. http://spark.apache.org

  187. Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J (2008) Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 41:706–716

    Article  PubMed  Google Scholar 

  188. Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM (2014) The EBI RDF platform: linked open data for the life sciences. Bioinformatics 30:1338–1339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Bootstraphttp://www.getbootstrap.com

  190. JQueryhttps://www.jquery.com

  191. Dojo Toolkithttps://dojotoolkit.org

  192. The Apache Lucenehttp://lucene.apache.org

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Acknowledgments

This work was supported by grants from the National Institutes of Health: U41HG007822 and P20GM103446.

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Authors and Affiliations

  1. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA

    Chuming Chen & Hongzhan Huang

  2. Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA

    Cathy H. Wu

  3. Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA

    Cathy H. Wu

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  1. Chuming Chen
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  2. Hongzhan Huang
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  3. Cathy H. Wu
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Correspondence to Chuming Chen .

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Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA

    Cathy H. Wu

  2. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA

    Cecilia N. Arighi

  3. Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA

    Karen E. Ross

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Chen, C., Huang, H., Wu, C.H. (2017). Protein Bioinformatics Databases and Resources. In: Wu, C., Arighi, C., Ross, K. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 1558. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6783-4_1

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  • DOI: https://doi.org/10.1007/978-1-4939-6783-4_1

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