{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T01:58:20Z","timestamp":1789869500416,"version":"4.0.1"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,8,11]],"date-time":"2016-08-11T00:00:00Z","timestamp":1470873600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,8,11]],"date-time":"2016-08-11T00:00:00Z","timestamp":1470873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Mutations in von Hippel-Lindau tumor suppressor protein (pVHL) predispose to develop tumors affecting specific target organs, such as the retina, epididymis, adrenal glands, pancreas and kidneys. Currently, more than 400\u2009pVHL interacting proteins are either described in the literature or predicted in public databases. This data is scattered among several different sources, slowing down the comprehension of pVHL\u2019s biological role. Here we present VHLdb, a novel database collecting available interaction and mutation data on pVHL to provide novel integrated annotations. In VHLdb, pVHL interactors are organized according to two annotation levels, manual and automatic. Mutation data are easily accessible and a novel visualization tool has been implemented. A user-friendly feedback function to improve database content through community-driven curation is also provided. VHLdb presently contains 478 interactors, of which 117 have been manually curated, and 1,074 mutations. This makes it the largest available database for pVHL-related information. VHLdb is available from URL:\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/vhldb.bio.unipd.it\/\">http:\/\/vhldb.bio.unipd.it\/<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1038\/srep31128","type":"journal-article","created":{"date-parts":[[2016,8,11]],"date-time":"2016-08-11T05:34:19Z","timestamp":1470893659000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["VHLdb: A database of von Hippel-Lindau protein interactors and mutations"],"prefix":"10.1038","volume":"6","author":[{"given":"Francesco","family":"Tabaro","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Minervini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faiza","family":"Sundus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Quaglia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanuela","family":"Leonardi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damiano","family":"Piovesan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvio C. E.","family":"Tosatto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,8,11]]},"reference":[{"key":"BFsrep31128_CR1","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1038\/ng0594-85","volume":"7","author":"JR Gnarra","year":"1994","unstructured":"Gnarra, J. R. et al. Mutations of the VHL tumour suppressor gene in renal carcinoma. Nat. Genet. 7, 85\u201390 (1994).","journal-title":"Nat. Genet."},{"key":"BFsrep31128_CR2","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nrc3844","volume":"15","author":"L Gossage","year":"2015","unstructured":"Gossage, L., Eisen, T. & Maher, E. R. VHL, the story of a tumour suppressor gene. Nat Rev Cancer 15, 55\u201364 (2015).","journal-title":"Nat Rev Cancer"},{"key":"BFsrep31128_CR3","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1038\/nature00767","volume":"417","author":"W-C Hon","year":"2002","unstructured":"Hon, W.-C. et al. Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. Nature 417, 975\u2013978 (2002).","journal-title":"Nature"},{"key":"BFsrep31128_CR4","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1002\/(SICI)1098-1004(1998)12:6<417::AID-HUMU8>3.0.CO;2-K","volume":"12","author":"C Stolle","year":"1998","unstructured":"Stolle, C. et al. Improved detection of germline mutations in the von Hippel-Lindau disease tumor suppressor gene. Hum. Mutat. 12, 417\u2013423 (1998).","journal-title":"Hum. Mutat."},{"key":"BFsrep31128_CR5","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1093\/hmg\/5.5.639","volume":"5","author":"FM Richards","year":"1996","unstructured":"Richards, F. M., Schofield, P. N., Fleming, S. & Maher, E. R. Expression of the von Hippel-Lindau disease tumour suppressor gene during human embryogenesis. Hum. Mol. Genet. 5, 639\u2013644 (1996).","journal-title":"Hum. Mol. Genet."},{"key":"BFsrep31128_CR6","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.1126\/science.7660130","volume":"269","author":"A Kibel","year":"1995","unstructured":"Kibel, A., Iliopoulos, O., DeCaprio, J. A. & Kaelin, W. G. Binding of the von Hippel-Lindau tumor suppressor protein to Elongin B and C. Science 269, 1444\u20131446 (1995).","journal-title":"Science"},{"key":"BFsrep31128_CR7","doi-asserted-by":"publisher","first-page":"12436","DOI":"10.1073\/pnas.96.22.12436","volume":"96","author":"K Iwai","year":"1999","unstructured":"Iwai, K. et al. Identification of the von Hippel-lindau tumor-suppressor protein as part of an active E3 ubiquitin ligase complex. Proc. Natl. Acad. Sci. USA 96, 12436\u201312441 (1999).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFsrep31128_CR8","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1126\/science.1059817","volume":"292","author":"M Ivan","year":"2001","unstructured":"Ivan, M. et al. HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing. Science 292, 464\u2013468 (2001).","journal-title":"Science"},{"key":"BFsrep31128_CR9","doi-asserted-by":"publisher","first-page":"pe30","DOI":"10.1126\/scisignal.124pe30","volume":"1","author":"IJ Frew","year":"2008","unstructured":"Frew, I. J. & Krek, W. pVHL: a multipurpose adaptor protein. Sci Signal 1, pe30 (2008).","journal-title":"Sci Signal"},{"key":"BFsrep31128_CR10","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.molcel.2011.11.031","volume":"45","author":"AM Gamper","year":"2012","unstructured":"Gamper, A. M. et al. Regulation of KLF4 Turnover Reveals an Unexpected Tissue-Specific Role of pVHL in Tumorigenesis. Molecular Cell 45, 233\u2013243 (2012).","journal-title":"Molecular Cell"},{"key":"BFsrep31128_CR11","doi-asserted-by":"crossref","unstructured":"Du, J. et al. pVHL Negatively Regulates Antiviral Signaling by Targeting MAVS for Proteasomal Degradation. J Immunol 1500588 doi: 10.4049\/jimmunol.1500588 (2015).","DOI":"10.4049\/jimmunol.1500588"},{"key":"BFsrep31128_CR12","doi-asserted-by":"publisher","first-page":"e35848","DOI":"10.1371\/journal.pone.0035848","volume":"7","author":"J Xue","year":"2012","unstructured":"Xue, J. et al. pVHL Mediates K63-Linked Ubiquitination of nCLU. PLoS ONE 7, e35848 (2012).","journal-title":"PLoS ONE"},{"key":"BFsrep31128_CR13","doi-asserted-by":"publisher","first-page":"3704","DOI":"10.1016\/j.febslet.2009.10.070","volume":"583","author":"E Leonardi","year":"2009","unstructured":"Leonardi, E., Murgia, a & Tosatto, S. C. E. Adding structural information to the von Hippel-Lindau (VHL) tumor suppressor interaction network. FEBS letters 583, 3704\u20133710 (2009).","journal-title":"FEBS letters"},{"key":"BFsrep31128_CR14","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1016\/S1097-2765(00)80096-9","volume":"1","author":"M Ohh","year":"1998","unstructured":"Ohh, M. et al. The von Hippel-Lindau tumor suppressor protein is required for proper assembly of an extracellular fibronectin matrix. Mol. Cell 1, 959\u2013968 (1998).","journal-title":"Mol. Cell"},{"key":"BFsrep31128_CR15","doi-asserted-by":"crossref","unstructured":"Tang, N., Mack, F. & Haase, V. pVHL function is essential for endothelial extracellular matrix deposition. Molecular and cellular \\ldots 26, (2006).","DOI":"10.1128\/MCB.26.7.2519-2530.2006"},{"key":"BFsrep31128_CR16","doi-asserted-by":"publisher","first-page":"5175","DOI":"10.1021\/pr200642c","volume":"10","author":"Y Lai","year":"2011","unstructured":"Lai, Y., Song, M., Hakala, K., Weintraub, S. T. & Shiio, Y. Proteomic dissection of the von Hippel-Lindau (VHL) interactome. J. Proteome Res. 10, 5175\u20135182 (2011).","journal-title":"J. Proteome Res."},{"key":"BFsrep31128_CR17","doi-asserted-by":"publisher","first-page":"e96986","DOI":"10.1371\/journal.pone.0096986","volume":"9","author":"G Minervini","year":"2014","unstructured":"Minervini, G. et al. Design and analysis of a Petri net model of the Von Hippel-Lindau (VHL) tumor suppressor interaction network. PLoS ONE 9, e96986 (2014).","journal-title":"PLoS ONE"},{"key":"BFsrep31128_CR18","doi-asserted-by":"publisher","first-page":"D841","DOI":"10.1093\/nar\/gkr1088","volume":"40","author":"S Kerrien","year":"2012","unstructured":"Kerrien, S. et al. The IntAct molecular interaction database in 2012. Nucleic Acids Res. 40, D841\u2013D846 (2012).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR19","doi-asserted-by":"crossref","unstructured":"Chesnel, F. et al. The von Hippel\u2013Lindau tumour suppressor gene: uncovering the expression of the pVHL172 isoform. Br J Cancer doi: 10.1038\/bjc.2015.189 (2015).","DOI":"10.1038\/bjc.2015.189"},{"key":"BFsrep31128_CR20","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1006\/geno.2000.6144","volume":"65","author":"ER Woodward","year":"2000","unstructured":"Woodward, E. R. et al. Comparative sequence analysis of the VHL tumor suppressor gene. Genomics 65, 253\u2013265 (2000).","journal-title":"Genomics"},{"key":"BFsrep31128_CR21","doi-asserted-by":"publisher","first-page":"D315","DOI":"10.1093\/nar\/gku982","volume":"43","author":"E Potenza","year":"2015","unstructured":"Potenza, E., Di Domenico, T., Walsh, I. & Tosatto, S. C. E. MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic Acids Res. 43, D315\u2013D320 (2015).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR22","doi-asserted-by":"publisher","first-page":"12605","DOI":"10.1038\/srep12605","volume":"5","author":"G Minervini","year":"2015","unstructured":"Minervini, G. et al. Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. Sci Rep 5, 12605 (2015).","journal-title":"Sci Rep"},{"key":"BFsrep31128_CR23","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1126\/science.8493574","volume":"260","author":"F Latif","year":"1993","unstructured":"Latif, F. et al. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science 260, 1317\u20131320 (1993).","journal-title":"Science"},{"key":"BFsrep31128_CR24","doi-asserted-by":"publisher","first-page":"e4897","DOI":"10.1371\/journal.pone.0004897","volume":"4","author":"H-CJ Shen","year":"2009","unstructured":"Shen, H.-C. J. et al. Deciphering von Hippel-Lindau (VHL\/Vhl)-associated pancreatic manifestations by inactivating Vhl in specific pancreatic cell populations. PLoS ONE 4, e4897 (2009).","journal-title":"PLoS ONE"},{"key":"BFsrep31128_CR25","doi-asserted-by":"publisher","first-page":"4991","DOI":"10.1200\/JCO.2004.05.061","volume":"22","author":"WY Kim","year":"2004","unstructured":"Kim, W. Y. & Kaelin, W. G. Role of VHL gene mutation in human cancer. J. Clin. Oncol. 22, 4991\u20135004 (2004).","journal-title":"J. Clin. Oncol."},{"key":"BFsrep31128_CR26","doi-asserted-by":"publisher","first-page":"7582","DOI":"10.1158\/1078-0432.CCR-09-2131","volume":"15","author":"AC Young","year":"2009","unstructured":"Young, A. C. et al. Analysis of VHL Gene Alterations and their Relationship to Clinical Parameters in Sporadic Conventional Renal Cell Carcinoma. Clin. Cancer Res. 15, 7582\u20137592 (2009).","journal-title":"Clin. Cancer Res."},{"key":"BFsrep31128_CR27","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.tibs.2005.06.009","volume":"30","author":"DR Fels","year":"2005","unstructured":"Fels, D. R. & Koumenis, C. HIF-1alpha and p53: the ODD couple? Trends Biochem. Sci. 30, 426\u2013429 (2005).","journal-title":"Trends Biochem. Sci."},{"key":"BFsrep31128_CR28","doi-asserted-by":"publisher","first-page":"2277","DOI":"10.4161\/cc.25371","volume":"12","author":"Y-S Jung","year":"2013","unstructured":"Jung, Y.-S. et al. Loss of VHL promotes progerin expression, leading to impaired p14\/ARF function and suppression of p53 activity. Cell Cycle 12, 2277\u20132290 (2013).","journal-title":"Cell Cycle"},{"key":"BFsrep31128_CR29","doi-asserted-by":"publisher","first-page":"2576","DOI":"10.1158\/0008-5472.CAN-05-3241","volume":"66","author":"EB Rankin","year":"2006","unstructured":"Rankin, E. B., Tomaszewski, J. E. & Haase, V. H. Renal cyst development in mice with conditional inactivation of the von Hippel-Lindau tumor suppressor. Cancer Res. 66, 2576\u20132583 (2006).","journal-title":"Cancer Res."},{"key":"BFsrep31128_CR30","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1038\/nm0895-822","volume":"1","author":"O Iliopoulos","year":"1995","unstructured":"Iliopoulos, O., Kibel, A., Gray, S. & Kaelin, W. G. Tumour suppression by the human von Hippel-Lindau gene product. Nat Med 1, 822\u2013826 (1995).","journal-title":"Nat Med"},{"key":"BFsrep31128_CR31","doi-asserted-by":"publisher","first-page":"D808","DOI":"10.1093\/nar\/gks1094","volume":"41","author":"A Franceschini","year":"2013","unstructured":"Franceschini, A. et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41, D808\u2013D815 (2013).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR32","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkj109","volume":"34","author":"C Stark","year":"2006","unstructured":"Stark, C. et al. BioGRID: a general repository for interaction datasets. Nucl. Acids Res. 34, D535\u2013D539 (2006).","journal-title":"Nucl. Acids Res"},{"key":"BFsrep31128_CR33","doi-asserted-by":"publisher","first-page":"3127","DOI":"10.1038\/onc.2011.40","volume":"30","author":"J-S Roe","year":"2011","unstructured":"Roe, J.-S., Kim, H.-R., Hwang, I.-Y., Cho, E.-J. & Youn, H.-D. von Hippel-Lindau protein promotes Skp2 destabilization on DNA damage. Oncogene 30, 3127\u20133138 (2011).","journal-title":"Oncogene"},{"key":"BFsrep31128_CR34","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.yexcr.2004.07.016","volume":"301","author":"MP Lolkema","year":"2004","unstructured":"Lolkema, M. P. et al. The von Hippel-Lindau tumor suppressor protein influences microtubule dynamics at the cell periphery. Exp. Cell Res. 301, 139\u2013146 (2004).","journal-title":"Exp. Cell Res."},{"key":"BFsrep31128_CR35","first-page":"521","volume":"31","author":"M Nordstrom-O\u2019Brien","year":"2010","unstructured":"Nordstrom-O\u2019Brien, M. et al. Genetic analysis of von Hippel-Lindau disease. Hum. Mutat. 31, 521\u2013537 (2010).","journal-title":"Hum. Mutat."},{"key":"BFsrep31128_CR36","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1111\/j.1469-1809.2011.00647.x","volume":"75","author":"E Leonardi","year":"2011","unstructured":"Leonardi, E., Martella, M., Tosatto, S. C. E. & Murgia, A. Identification and in silico analysis of novel von Hippel-Lindau (VHL) gene variants from a large population. Ann. Hum. Genet. 75, 483\u2013496 (2011).","journal-title":"Ann. Hum. Genet."},{"key":"BFsrep31128_CR37","doi-asserted-by":"publisher","first-page":"5500","DOI":"10.1158\/0008-5472.CAN-11-0757","volume":"71","author":"MP Rechsteiner","year":"2011","unstructured":"Rechsteiner, M. P. et al. VHL gene mutations and their effects on hypoxia inducible factor HIF\u03b1: identification of potential driver and passenger mutations. Cancer Res. 71, 5500\u20135511 (2011).","journal-title":"Cancer Res."},{"key":"BFsrep31128_CR38","doi-asserted-by":"publisher","first-page":"D805","DOI":"10.1093\/nar\/gku1075","volume":"43","author":"SA Forbes","year":"2015","unstructured":"Forbes, S. A. et al. COSMIC: exploring the world\u2019s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805\u2013D811 (2015).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR39","doi-asserted-by":"publisher","first-page":"1977","DOI":"10.7314\/APJCP.2015.16.5.1977","volume":"16","author":"B Zhang","year":"2015","unstructured":"Zhang, B. et al. VHL gene mutation analysis of a Chinese family with non- syndromic pheochromocytomas and patients with apparently sporadic pheochromocytoma. Asian Pac. J. Cancer Prev. 16, 1977\u20131980 (2015).","journal-title":"Asian Pac. J. Cancer Prev."},{"key":"BFsrep31128_CR40","first-page":"9872594","volume":"2016","author":"G Arunachal","year":"2016","unstructured":"Arunachal, G. et al. Molecular Characterization of a Novel Germline VHL Mutation by Extensive In Silico Analysis in an Indian Family with Von Hippel-Lindau Disease. Genet Res Int 2016, 9872594 (2016).","journal-title":"Genet Res Int"},{"key":"BFsrep31128_CR41","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1111\/j.1399-0004.2010.01464.x","volume":"79","author":"AD Sorrell","year":"2011","unstructured":"Sorrell, A. D. et al. Clinical and functional properties of novel VHL mutation (X214L) consistent with Type 2A phenotype and low risk of renal cell carcinoma. Clin. Genet. 79, 539\u2013545 (2011).","journal-title":"Clin. Genet."},{"key":"BFsrep31128_CR42","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch, W. & Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577\u20132637 (1983).","journal-title":"Biopolymers"},{"key":"BFsrep31128_CR43","doi-asserted-by":"publisher","first-page":"2189","DOI":"10.1093\/bioinformatics\/bts343","volume":"28","author":"I Walsh","year":"2012","unstructured":"Walsh, I. et al. Bluues server: electrostatic properties of wild-type and mutated protein structures. Bioinformatics 28, 2189\u20132190 (2012).","journal-title":"Bioinformatics"},{"key":"BFsrep31128_CR44","doi-asserted-by":"publisher","first-page":"S7","DOI":"10.1186\/1471-2164-15-S4-S7","volume":"15","author":"M Giollo","year":"2014","unstructured":"Giollo, M., Martin, A. J., Walsh, I., Ferrari, C. & Tosatto, S. C. NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation. BMC Genomics 15 Suppl 4, S7 (2014).","journal-title":"BMC Genomics"},{"key":"BFsrep31128_CR45","doi-asserted-by":"publisher","first-page":"D470","DOI":"10.1093\/nar\/gku1204","volume":"43","author":"A Chatr-Aryamontri","year":"2015","unstructured":"Chatr-Aryamontri, A. et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 43, D470\u2013D478 (2015).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR46","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1038\/ng0704-664","volume":"36","author":"R Hoffmann","year":"2004","unstructured":"Hoffmann, R. & Valencia, A. A gene network for navigating the literature. Nat. Genet. 36, 664 (2004).","journal-title":"Nat. Genet."},{"key":"BFsrep31128_CR47","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1093\/bioinformatics\/bti115","volume":"21","author":"P Pagel","year":"2005","unstructured":"Pagel, P. et al. The MIPS mammalian protein\u2013protein interaction database. Bioinformatics 21, 832\u2013834 (2005).","journal-title":"Bioinformatics"},{"key":"BFsrep31128_CR48","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nmeth.1931","volume":"9","author":"S Orchard","year":"2012","unstructured":"Orchard, S. et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Meth 9, 345\u2013350 (2012).","journal-title":"Nat Meth"},{"key":"BFsrep31128_CR49","doi-asserted-by":"publisher","first-page":"D204","DOI":"10.1093\/nar\/gku989","volume":"43","author":"TU Consortium","year":"2015","unstructured":"Consortium, T. U. UniProt: a hub for protein information. Nucl. Acids Res. 43, D204\u2013D212 (2015).","journal-title":"Nucl. Acids Res"},{"key":"BFsrep31128_CR50","doi-asserted-by":"publisher","first-page":"D301","DOI":"10.1093\/nar\/gkl971","volume":"35","author":"H Berman","year":"2007","unstructured":"Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35, D301\u2013D303 (2007).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR51","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25\u201329 (2000).","journal-title":"Nat. Genet."},{"key":"BFsrep31128_CR52","doi-asserted-by":"publisher","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","volume":"44","author":"RD Finn","year":"2016","unstructured":"Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future. Nucl. Acids Res. 44, D279\u2013D285 (2016).","journal-title":"Nucl. Acids Res"},{"key":"BFsrep31128_CR53","doi-asserted-by":"publisher","first-page":"D7","DOI":"10.1093\/nar\/gkt1146","volume":"42","author":"A Acland","year":"2014","unstructured":"Acland, A. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 42, D7\u2013D17 (2014).","journal-title":"Nucleic Acids Res"},{"key":"BFsrep31128_CR54","doi-asserted-by":"publisher","first-page":"W529","DOI":"10.1093\/nar\/gkq399","volume":"38","author":"H Ashkenazy","year":"2010","unstructured":"Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38, W529\u2013W533 (2010).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR55","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1007\/978-1-59745-398-1_30","volume":"484","author":"O Keskin","year":"2008","unstructured":"Keskin, O., Nussinov, R. & Gursoy, A. PRISM: protein-protein interaction prediction by structural matching. Methods Mol. Biol. 484, 505\u2013521 (2008).","journal-title":"Methods Mol. Biol."},{"key":"BFsrep31128_CR56","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1002\/prot.20617","volume":"61","author":"V Chelliah","year":"2005","unstructured":"Chelliah, V., Blundell, T. & Mizuguchi, K. Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition. Proteins 61, 722\u2013731 (2005).","journal-title":"Proteins"},{"key":"BFsrep31128_CR57","doi-asserted-by":"publisher","first-page":"D259","DOI":"10.1093\/nar\/gkt1047","volume":"42","author":"H Dinkel","year":"2014","unstructured":"Dinkel, H. et al. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res. 42, D259\u2013D266 (2014).","journal-title":"Nucleic Acids Res."},{"key":"BFsrep31128_CR58","unstructured":"Marco Biasini. PV-WebGL-based protein viewer. doi: 10.5281\/zenodo.12620 (2014)."},{"key":"BFsrep31128_CR59","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1101\/gr.157602.113","volume":"23","author":"DA Wheeler","year":"2013","unstructured":"Wheeler, D. A. & Wang, L. From human genome to cancer genome: The first decade. Genome Res. 23, 1054\u20131062 (2013).","journal-title":"Genome Res."},{"key":"BFsrep31128_CR60","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.semcancer.2014.04.002","volume":"30","author":"E Wang","year":"2015","unstructured":"Wang, E. et al. Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data. Seminars in Cancer Biology 30, 4\u201312 (2015).","journal-title":"Seminars in Cancer Biology"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep31128","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep31128.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep31128.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,4]],"date-time":"2023-01-04T16:13:55Z","timestamp":1672848835000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep31128"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8,11]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,11,14]]}},"alternative-id":["BFsrep31128"],"URL":"https:\/\/doi.org\/10.1038\/srep31128","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8,11]]},"assertion":[{"value":"14 May 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 July 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 August 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"31128"}}