{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T07:12:21Z","timestamp":1783667541084,"version":"3.55.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Synthetic fusion proteins have shown great potential in various biotechnological and (bio)pharmaceutical applications. They usually contain more than two protein domains joined by a linker peptide sequence which is often selected intuitively or in ad hoc manner. Thus, we developed an integrated web-based system, SynLinker, to provide appropriate linker candidates for constructing fusion proteins. We compiled a total of 2260 linker sequences comprising of natural linkers extracted from a set of non-redundant multi-domain proteins in Protein Data Bank and artificial\/empirical linkers collected from literature and patents. Multiple query interface allows users to search for the desired linker candidates based on selection criteria and their preferences. In addition, a selected linker can be combined with two domain structures which are uploaded and appended at its N and C terminals, thereby predicting a de novo structure of the fusion protein. Hence, SynLinker can serve as a systematic tool for researchers who are interested in designing synthetic fusion proteins.<\/jats:p>\n               <jats:p>Availability and implementation: SynLinker is freely available at http:\/\/bioinfo.bti.a-star.edu.sg\/synlinker.<\/jats:p>\n               <jats:p>Contact: cheld@nus.edu.sg<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv447","type":"journal-article","created":{"date-parts":[[2015,7,30]],"date-time":"2015-07-30T23:59:41Z","timestamp":1438300781000},"page":"3700-3702","source":"Crossref","is-referenced-by-count":41,"title":["SynLinker: an integrated system for designing linkers and synthetic fusion proteins"],"prefix":"10.1093","volume":"31","author":[{"given":"Chengcheng","family":"Liu","sequence":"first","affiliation":[{"name":"1 Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ju Xin","family":"Chin","sequence":"additional","affiliation":[{"name":"1 Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Yup","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore 138668, Singapore,"},{"name":"2 Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore and"},{"name":"3 NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,7,29]]},"reference":[{"key":"2023020202410777700_btv447-B1","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s11095-008-9767-0","article-title":"Insertion of the designed helical linker led to increased expression of tf-based fusion proteins","volume":"26","author":"Amet","year":"2009","journal-title":"Pharm. Res."},{"key":"2023020202410777700_btv447-B2","doi-asserted-by":"crossref","first-page":"7292","DOI":"10.1073\/pnas.0500062102","article-title":"Recombinant granulocyte colony-stimulating factor-transferrin fusion protein as an oral myelopoietic agent","volume":"102","author":"Bai","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020202410777700_btv447-B3","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1016\/j.addr.2012.09.039","article-title":"Fusion protein linkers: property, design and functionality","volume":"65","author":"Chen","year":"2012","journal-title":"Adv. Drug Deliv. 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Pept."},{"key":"2023020202410777700_btv447-B7","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1002\/(SICI)1097-0134(20000501)39:2<112::AID-PROT2>3.0.CO;2-B","article-title":"A fast method to sample real protein conformational space","volume":"39","author":"Feldman","year":"2000","journal-title":"Proteins"},{"key":"2023020202410777700_btv447-B8","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1093\/protein\/15.11.871","article-title":"An analysis of protein domain linkers: their classification and role in protein folding","volume":"15","author":"George","year":"2002","journal-title":"Protein Eng."},{"key":"2023020202410777700_btv447-B9","doi-asserted-by":"crossref","first-page":"W562","DOI":"10.1093\/nar\/gkh422","article-title":"LINKER: a web server to generate peptide sequences with extended conformation","volume":"32","author":"Xue","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023020202410777700_btv447-B10","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.biotechadv.2014.11.005","article-title":"Synthetic fusion protein design and applications","volume":"33","author":"Yu","year":"2015","journal-title":"Biotechnol. Adv."},{"key":"2023020202410777700_btv447-B11","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1016\/j.pnsc.2008.12.007","article-title":"Design and optimization of a linker for fusion protein construction","volume":"19","author":"Zhang","year":"2009","journal-title":"Prog. Nat. Sci."},{"key":"2023020202410777700_btv447-B12","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.pep.2008.04.013","article-title":"Increasing the homogeneity, stability and activity of human serum albumin and interferon-alpha2b fusion protein by linker engineering","volume":"61","author":"Zhao","year":"2008","journal-title":"Protein Exp. Purif."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/22\/3700\/49036035\/bioinformatics_31_22_3700.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/22\/3700\/49036035\/bioinformatics_31_22_3700.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:55:57Z","timestamp":1675310157000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/22\/3700\/241706"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,7,29]]},"references-count":12,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2015,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv447","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,11,15]]},"published":{"date-parts":[[2015,7,29]]}}}