{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T10:40:35Z","timestamp":1684060835207},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Cage-shaped protein, with its special structure, may have potential applications in biomedicine and nanotechnology. We developed a program CSPro (Cage-Shaped Protein) for efficient identification of cage-shaped proteins based on quaternary structure. CSPro is capable of revealing the corresponding cage-shaped feature more clearly and quickly than traditional visualization tools. Using CSPro, we have searched the full set of PDB (protein data bank) and three types of proteins are retrieved with notably large central cavities inside. CSPro can be used to validate if the quaternary structure of a protein is cage shaped in molecular simulation.<\/jats:p><jats:p>Availability: \u00a0http:\/\/www.cad.zju.edu.cn\/home\/humin<\/jats:p><jats:p>Contact: \u00a0humin@cad.zju.edu.cn<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm476","type":"journal-article","created":{"date-parts":[[2007,10,6]],"date-time":"2007-10-06T00:14:42Z","timestamp":1191629682000},"page":"3400-3402","source":"Crossref","is-referenced-by-count":1,"title":["Identification and visualization of cage-shaped proteins"],"prefix":"10.1093","volume":"23","author":[{"given":"Min","family":"Hu","sequence":"first","affiliation":[{"name":"1 State Key Laboratory of CAD & CG and 2College of Life Sciences, Zhejiang University, Hangzhou, 310058, China"}]},{"given":"Junhui","family":"Wang","sequence":"additional","affiliation":[{"name":"1 State Key Laboratory of CAD & CG and 2College of Life Sciences, Zhejiang University, Hangzhou, 310058, China"}]},{"given":"Qunsheng","family":"Peng","sequence":"additional","affiliation":[{"name":"1 State Key Laboratory of CAD & CG and 2College of Life Sciences, Zhejiang University, Hangzhou, 310058, China"}]}],"member":"286","published-online":{"date-parts":[[2007,10,5]]},"reference":[{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucl. Acids Res"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.jmgm.2006.02.012","article-title":"Efficient molecular surface generation using level-set methods","volume":"25","author":"Can","year":"2006","journal-title":"J. Mol. Graph. Model"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/442360a","article-title":"Protein folding inside the cage","volume":"442","author":"Ellis","year":"2006","journal-title":"Nature"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/1049-9652(92)90070-E","article-title":"Discrete multidimensional Jordan surfaces","volume":"54","author":"Herman","year":"1992","journal-title":"CVGIP-Graph. Model. Image process"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1007\/BF00117400","article-title":"Cavity search: an algorithm for the isolation and display of cavity-like binding regions","volume":"4","author":"Ho","year":"1990","journal-title":"J. Comput. Aided. Mol. Des"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD \u2013 Visual Molecular Dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/71236","article-title":"The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site","volume":"7","author":"Ilari","year":"2000","journal-title":"Nat. Struct. Biol"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/0734-189X(89)90147-3","article-title":"Digital topology: introduction and survey","volume":"48","author":"Kong","year":"1989","journal-title":"Comput. Vison Graph"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1107\/S0021889891004399","article-title":"MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures","volume":"24","author":"Kraulis","year":"1991","journal-title":"J. Appl. Cryst"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/0166-8641(92)90019-V","article-title":"The topology of digital images","volume":"46","author":"Kronheimer","year":"1992","journal-title":"Topol. Appl"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/0022-2836(71)90324-X","article-title":"The interpretation of protein structures: estimation of static accessibility","volume":"55","author":"Lee","year":"1971","journal-title":"J. Mol. Biol"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O","article-title":"Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape","volume":"33","author":"Liang","year":"1998","journal-title":"Proteins"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"10403","DOI":"10.1073\/pnas.96.18.10403","article-title":"Epoxomicin, a potent and selective proteasome inhibitor, exhibits in vivo antiinflammatory activity","volume":"96","author":"Meng","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1002\/jcc.540120405","article-title":"A rapid finite difference algorithm, utilising succesive over relaxation to solve the Poisson\u2013Boltzmann equation","volume":"12","author":"Nicholls","year":"1991","journal-title":"J. Comput. Chem"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1021\/ci00049a002","article-title":"A simple method for the representation, quantification, and comparison of the volumes and shapes of chemical compounds","volume":"26","author":"Stouch","year":"1986","journal-title":"J. Chem. Inf. Comput. Sci"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1016\/j.cell.2006.04.027","article-title":"Structural features of the GroEL-GroES nano-cage required for rapid folding of encapsulated protein","volume":"125","author":"Tang","year":"2006","journal-title":"Cell"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1246\/bcsj.78.2075","article-title":"Synthesis of CoB3BOB4B nanoparticles using the cage-shaped protein, Apoferritin","volume":"78","author":"Tsukamoto","year":"2005","journal-title":"Bull. Chem. Soc. Jpn"},{"key":"2023041107444139200_","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1042\/bj3490783","article-title":"Iron oxidation and hydrolysis reactions of a novel ferritin from Listeria innocua","volume":"349","author":"Yang","year":"2000","journal-title":"Biochem. J"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/24\/3400\/49823058\/bioinformatics_23_24_3400.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/24\/3400\/49823058\/bioinformatics_23_24_3400.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,14]],"date-time":"2023-05-14T10:06:01Z","timestamp":1684058761000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/24\/3400\/263220"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,10,5]]},"references-count":18,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2007,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm476","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,12,15]]},"published":{"date-parts":[[2007,10,5]]}}}