{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T21:29:07Z","timestamp":1762032547385},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The object of this study is to propose a new method to identify small compact units that compose protein three-dimensional structures. These fragments, called \u2018protein units (PU)\u2019, are a new level of description to well understand and analyze the organization of protein structures. The method only works from the contact probability matrix, i.e. the inter C\u03b1-distances translated into probabilities. It uses the principle of conventional hierarchical clustering, leading to a series of nested partitions of the 3D structure. Every step aims at dividing optimally a unit into 2 or 3 subunits according to a criterion called \u2018partition index\u2019 assessing the structural independence of the subunits newly defined. Moreover, an entropy-derived squared correlation R is used for assessing globally the protein structure dissection. The method is compared to other splitting algorithms and shows relevant performance.<\/jats:p>\n               <jats:p>Availability: An Internet server with dedicated tools is available at<\/jats:p>\n               <jats:p>Contact: \u00a0debrevern@ebgm.jussieu.fr.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti773","type":"journal-article","created":{"date-parts":[[2005,11,15]],"date-time":"2005-11-15T01:12:33Z","timestamp":1132017153000},"page":"129-133","source":"Crossref","is-referenced-by-count":30,"title":["\u2018Protein Peeling\u2019: an approach for splitting a 3D protein structure into compact fragments"],"prefix":"10.1093","volume":"22","author":[{"given":"Jean-Christophe","family":"Gelly","sequence":"first","affiliation":[{"name":"INSERM U726, Equipe de Bioinformatique G\u00e9nomique & Mol\u00e9culaire (EBGM), Universit\u00e9 Denis Diderot\u2014Paris 7 1 \u00a0 1 \u00a0 \u00a0 case 7113, 75251 Paris Cedex 05, France"},{"name":"UMR CNRS 7602, Institut de Min\u00e9ralogie et Physique des Milieux Condens\u00e9s (IMPMC), Universit\u00e9 Pierre & Marie Curie 2 \u00a0 2 \u00a0 \u00a0 4, Place Jussieu, 75252 Paris Cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandre G.","family":"de Brevern","sequence":"additional","affiliation":[{"name":"INSERM U726, Equipe de Bioinformatique G\u00e9nomique & Mol\u00e9culaire (EBGM), Universit\u00e9 Denis Diderot\u2014Paris 7 1 \u00a0 1 \u00a0 \u00a0 case 7113, 75251 Paris Cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Serge","family":"Hazout","sequence":"additional","affiliation":[{"name":"INSERM U726, Equipe de Bioinformatique G\u00e9nomique & Mol\u00e9culaire (EBGM), Universit\u00e9 Denis Diderot\u2014Paris 7 1 \u00a0 1 \u00a0 \u00a0 case 7113, 75251 Paris Cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,11,14]]},"reference":[{"key":"2023012408302097700_b1","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1093\/bioinformatics\/btg006","article-title":"PDP: protein domain parser","volume":"19","author":"Alexandrov","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408302097700_b2","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":"Nucleic Acids Res."},{"key":"2023012408302097700_b3","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1146\/annurev.bi.59.070190.005043","article-title":"The classification and origins of protein folding patterns","volume":"59","author":"Chothia","year":"1990","journal-title":"Annu. 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