{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:51:49Z","timestamp":1775980309688,"version":"3.50.1"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,7,11]],"date-time":"2021-07-11T00:00:00Z","timestamp":1625961600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Research Council Executive Agency","award":["640283"],"award-info":[{"award-number":["640283"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geometry can lead to more adequate predictions of their interactions. In the present work, we assess the performance of reference shape retrieval methods from the computer vision community on protein shapes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Shape retrieval methods are efficient in identifying orthologous proteins and tracking large conformational changes. This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that (i) abstracts the underlying protein sequence, structure or fold, (ii) allows the use of shape retrieval methods to screen large databases of protein structures to identify surficial homologs and possible interacting partners and (iii) opens an extension of the protein structure\u2013function paradigm toward a protein structure-surface(s)-function paradigm.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>All data are available online at http:\/\/datasetmachat.drugdesign.fr.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab511","type":"journal-article","created":{"date-parts":[[2021,7,8]],"date-time":"2021-07-08T19:21:22Z","timestamp":1625772082000},"page":"4375-4382","source":"Crossref","is-referenced-by-count":5,"title":["Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics"],"prefix":"10.1093","volume":"37","author":[{"given":"Mohamed","family":"Machat","sequence":"first","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]},{"given":"Florent","family":"Langenfeld","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]},{"given":"Daniela","family":"Craciun","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]},{"given":"L\u00e9a","family":"Sirugue","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]},{"given":"Taoufik","family":"Labib","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]},{"given":"Nathalie","family":"Lagarde","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]},{"given":"Maxime","family":"Maria","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"},{"name":"Laboratoire XLIM, UMR CNRS 7252, Universit\u00e9 de Limoges , Limoges 87000, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5921-460X","authenticated-orcid":false,"given":"Matthieu","family":"Montes","sequence":"additional","affiliation":[{"name":"Laboratoire GBCM, EA 7528, Conservatoire National des Arts et M\u00e9tiers, Hesam Universit\u00e9 , Paris 75003, France"}]}],"member":"286","published-online":{"date-parts":[[2021,7,11]]},"reference":[{"key":"2023061310544836300_btab511-B1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1109\/MRA.2012.2206675","article-title":"Tutorial: point cloud library: three-dimensional object recognition and 6 DOF pose estimation","volume":"19","author":"Aldoma","year":"2012","journal-title":"IEEE Robot. 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