{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T20:16:35Z","timestamp":1762460195580,"version":"3.41.2"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,21]],"date-time":"2024-02-21T00:00:00Z","timestamp":1708473600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004794","name":"Centre National de la Recherche Scientifique","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004794","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Universit\u00e9 C\u00f4te d'Azur"},{"DOI":"10.13039\/501100001677","name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"French National Research Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Popular shape-based alignment methods handle molecular flexibility by utilizing conformational ensembles to select the most fitted conformer. However, the initial conformer library generation step is computationally intensive and limiting to the overall alignment process. In this work, we describe a method to perform flexible alignment of two molecular shapes by optimizing the 3D conformation. SENSAAS-Flex, an add-on to the SENSAAS tool, is able to proceed from a limited set of initial conformers through an iterative process where additional conformational optimizations are made at the substructure level and constrained by the target shape.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In self- and cross-alignment experiments, SENSAAS-Flex is able to reproduce the crystal structure geometry of ligands of the AstraZeneca Molecule Overlay Test set and PDBbind refined dataset. Our study shows that the point-based representation of molecular surfaces is appropriate in terms of shape constraint to sample the conformational space and perform flexible molecular alignments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The documentation and source code are available at https:\/\/chemoinfo.ipmc.cnrs.fr\/Sensaas-flex\/sensaas-flex-main.tar.gz<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae105","type":"journal-article","created":{"date-parts":[[2024,2,22]],"date-time":"2024-02-22T01:49:05Z","timestamp":1708566545000},"source":"Crossref","is-referenced-by-count":2,"title":["SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space"],"prefix":"10.1093","volume":"40","author":[{"given":"Hamza","family":"Biyuzan","sequence":"first","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, CNRS UMR7271, I3S , Sophia Antipolis 06900, France"}]},{"given":"Mohamed-Akram","family":"Masrour","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, CNRS UMR7271, I3S , Sophia Antipolis 06900, France"}]},{"given":"Lucas","family":"Grandmougin","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, CNRS UMR7271, I3S , Sophia Antipolis 06900, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9885-6445","authenticated-orcid":false,"given":"Fr\u00e9d\u00e9ric","family":"Payan","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, CNRS UMR7271, I3S , Sophia Antipolis 06900, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6209-6464","authenticated-orcid":false,"given":"Dominique","family":"Douguet","sequence":"additional","affiliation":[{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, Inserm U1323, CNRS UMR7275, IPMC , Valbonne 06560, France"}]}],"member":"286","published-online":{"date-parts":[[2024,2,21]]},"reference":[{"key":"2024030710490451600_btae105-B1","doi-asserted-by":"crossref","first-page":"2887","DOI":"10.1021\/jm9602928","article-title":"The properties of known drugs. 1. 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