{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:25:51Z","timestamp":1763810751052,"version":"3.41.2"},"reference-count":21,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:00:00Z","timestamp":1646092800000},"content-version":"vor","delay-in-days":59,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board, India","doi-asserted-by":"crossref","award":["JC Bose Fellowship (SB\/S2\/JC-071\/2015)"],"award-info":[{"award-number":["JC Bose Fellowship (SB\/S2\/JC-071\/2015)"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Department of Biotechnology , Ministry of Science and Technology, India","award":["Bioinformatics Centre Grant (BT\/PR40187\/BTIS\/137\/9"],"award-info":[{"award-number":["Bioinformatics Centre Grant (BT\/PR40187\/BTIS\/137\/9"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Disulphide bonds are stabilizing crosslinks in proteins and serve to enhance their thermal stability. In proteins that are small and rich in disulphide bonds, they could be the major determining factor for the choice of conformational state since their constraints on appropriate backbone conformation can be substantial. Such crosslinks and their positional conservation could itself enable protein family and functional association. Despite the importance of the field, there is no comprehensive database on disulphide crosslinks that is available to the public. Herein we provide information on disulphides in DSDBASE2.0, an updated and significantly expanded database that is freely available, fully annotated and manually curated database on native and modelled disulphides. The web interface also provides several useful computational tools that have been specifically developed for proteins containing disulphide crosslinks. The modelling of disulphide crosslinks is performed using stereochemical criteria, coded within our Modelling of Disulphides in Proteins (MODIP) algorithm. The inclusion of modelled disulphides potentially enhances the loop database substantially, thereby permitting the recognition of compatible polypeptide segments that could serve as templates for immediate modelling. The DSDBASE2.0 database has been updated to include 153,944 PDB entries, 216,096 native and 20,153,850 modelled disulphide bond segments from PDB January 2021 release. The current database also provides a resource to user-friendly search for multiple disulphide bond containing loops, along with annotation of their function using GO and subcellular localization of the query. Furthermore, it is possible to obtain the three-dimensional models of disulphide-rich small proteins using an independent algorithm, RANMOD, that generates and examines random, but allowed backbone conformations of the polypeptide. DSDBASE2.0 still remains the largest open-access repository that organizes all disulphide bonds of proteins on a single platform. The database can be accessed from http:\/\/caps.ncbs.res.in\/dsdbase2.<\/jats:p>","DOI":"10.1093\/database\/baac005","type":"journal-article","created":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T12:08:07Z","timestamp":1644581287000},"source":"Crossref","is-referenced-by-count":6,"title":["DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins"],"prefix":"10.1093","volume":"2022","author":[{"given":"Neha V","family":"Kalmankar","sequence":"first","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), GKVK Campus, Bellary Road, Bengaluru, Karnataka 560065, India"},{"name":"The University of Trans-Disciplinary Health Sciences and Technology (TDU), #74\/2, Jarakabande Kaval, Post Attur, Via Yelahanka, Bengaluru, Karnataka 560064, India"}]},{"given":"Murugavel","family":"Pavalam","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), GKVK Campus, Bellary Road, Bengaluru, Karnataka 560065, India"}]},{"given":"Sowmya","family":"Indrakumar","sequence":"additional","affiliation":[{"name":"Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India"}]},{"given":"Narayanaswamy","family":"Srinivasan","sequence":"additional","affiliation":[{"name":"Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6642-2367","authenticated-orcid":false,"given":"Ramanathan","family":"Sowdhamini","sequence":"additional","affiliation":[{"name":"National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), GKVK Campus, Bellary Road, Bengaluru, Karnataka 560065, India"},{"name":"Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India"},{"name":"Institute of Bioinformatics and Applied Biotechnology, Biotech Park, GN Ramachandran Road, Electronics City Phase 1, Bengaluru, Karnataka 560100, India"}]}],"member":"286","published-online":{"date-parts":[[2022,3,1]]},"reference":[{"key":"2022031007345783100_R1","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/0022-2836(81)90515-5","article-title":"Disulphide bridges in globular proteins","volume":"151","author":"Thornton","year":"1981","journal-title":"J. Mol. Biol."},{"key":"2022031007345783100_R2","doi-asserted-by":"publisher","first-page":"5222","DOI":"10.1021\/ja01601a025","article-title":"Theory of elastic mechanisms in fibrous proteins","volume":"78","author":"Flory","year":"1956","journal-title":"J. Am. Chem. Soc."},{"key":"2022031007345783100_R3","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.febslet.2013.11.024","article-title":"Protein disulfide engineering","volume":"588","author":"Dombkowski","year":"2014","journal-title":"FEBS Lett."},{"key":"2022031007345783100_R4","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1002\/pmic.200300745","article-title":"Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network","volume":"4","author":"Martelli","year":"2004","journal-title":"Proteomics"},{"key":"2022031007345783100_R5","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2022031007345783100_R6","doi-asserted-by":"publisher","first-page":"D200","DOI":"10.1093\/nar\/gkh026","article-title":"DSDBASE: a consortium of native and modelled disulphide bonds in proteins","volume":"32","author":"Vinayagam","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2022031007345783100_R7","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1093\/protein\/6.8.873","article-title":"Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of \u03b1-conotoxin gi and edothelin I","volume":"6","author":"Sowdhamini","year":"1993","journal-title":"Protein Eng. Des. Sel."},{"key":"2022031007345783100_R8","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-346","article-title":"Disulfide by design 2.0: a web-based tool for disulfide engineering in proteins","volume":"14","author":"Craig","year":"2013","journal-title":"BMC Bioinform."},{"key":"2022031007345783100_R9","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1093\/protein\/2.2.119","article-title":"Model building of disulfide bonds in proteins with known three-dimensional structure","volume":"2","author":"Hazes","year":"1988","journal-title":"Protein Eng. Des. Sel."},{"key":"2022031007345783100_R10","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1093\/protein\/3.2.95","article-title":"Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis","volume":"3","author":"Sowdhamini","year":"1989","journal-title":"Protein Eng. Des. Sel."},{"key":"2022031007345783100_R11","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1110\/ps.9.4.776","article-title":"Novel disulfide engineering in human carbonic anhydrase II using the PAIRWISE side-chain geometry database","volume":"9","author":"Burton","year":"2000","journal-title":"Protein Sci."},{"key":"2022031007345783100_R12","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/protein\/gzu017","article-title":"Structure-based approach to the prediction of disulfide bonds in proteins","volume":"27","author":"Salam","year":"2014","journal-title":"Protein Eng. Des. 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Genet."},{"key":"2022031007345783100_R14","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1021\/bi00003a019","article-title":"Structural comparison of two major endo-1,4-Xylanases from Trichoderma reesei","volume":"34","author":"T\u00f6rr\u00f6nen","year":"1995","journal-title":"Biochemistry"},{"key":"2022031007345783100_R15","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1007\/s00792-004-0400-9","article-title":"Engineering the thermostability of Trichoderma reesei endo-1,4-\u03b2- xylanase II by combination of disulphide bridges","volume":"8","author":"Xiong","year":"2004","journal-title":"Extremophiles"},{"key":"2022031007345783100_R16","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1006\/jmbi.1999.3383","article-title":"Plant cyclotides: a unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif","volume":"294","author":"Craik","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2022031007345783100_R17","first-page":"251","article-title":"The cyclotides: Novel macrocyclic peptides as scaffolds in drug design","volume":"5","author":"Craik","year":"2002","journal-title":"Curr. Opin. Drug Discov. Dev"},{"key":"2022031007345783100_R18","doi-asserted-by":"publisher","first-page":"2354","DOI":"10.1002\/cbic.200900342","article-title":"The conserved glu in the cyclotide cycloviolacin O2 has a key structural role","volume":"10","author":"G\u00f6ransson","year":"2009","journal-title":"ChemBioChem"},{"key":"2022031007345783100_R19","doi-asserted-by":"publisher","first-page":"11510","DOI":"10.1021\/acs.chemrev.9b00207","article-title":"Conotoxins: chemistry and biology","volume":"119","author":"Jin","year":"2019","journal-title":"Chem. Rev."},{"key":"2022031007345783100_R20","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.peptides.2011.10.026","article-title":"Pc16a, the first characterized peptide from Conus pictus venom, shows a novel disulfide connectivity","volume":"34","author":"Van Der Haegen","year":"2012","journal-title":"Peptides"},{"key":"2022031007345783100_R21","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1042\/BJ20120548","article-title":"Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides","volume":"446","author":"Oparin","year":"2012","journal-title":"Biochem. J."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac005\/42793419\/baac005.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baac005\/42793419\/baac005.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T07:35:19Z","timestamp":1646897719000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baac005\/6540159"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,1]]},"references-count":21,"URL":"https:\/\/doi.org\/10.1093\/database\/baac005","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2022,1,1]]},"article-number":"baac005"}}