{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T01:43:23Z","timestamp":1785894203623,"version":"3.56.0"},"reference-count":2,"publisher":"Oxford University Press (OUP)","issue":"5","funder":[{"name":"Airc-Italy","award":["IG10740"],"award-info":[{"award-number":["IG10740"]}]},{"name":"Telethon-Italy","award":["S00068TELC"],"award-info":[{"award-number":["S00068TELC"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We developed a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy (i.e. PSN-ENM) to investigate structural communication in biomacromolecules. The approach starts from a Protein Structure Graph and searches for all shortest communication pathways between user-specified residues. The graph is computed on a single preferably high-resolution structure. Information on system\u2019s dynamics is supplied by ENM-NMA.<\/jats:p>\n               <jats:p>The PSN\u2013ENM methodology is made of multiple steps both in the setup and analysis stages, which may discourage inexperienced users. To facilitate its usage, we implemented WebPSN, a freely available web server that allows the user to easily setup the calculation, perform post-processing analyses and both visualize and download numerical and 3D representations of the output. Speed and accuracy make this server suitable to investigate structural communication, including allosterism, in large sets of bio-macromolecular systems.<\/jats:p>\n               <jats:p>Availability and implementation: The WebPSN server is freely available at http:\/\/webpsn.hpc.unimore.it.<\/jats:p>\n               <jats:p>Contact: \u00a0fanelli@unimo.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu718","type":"journal-article","created":{"date-parts":[[2014,10,30]],"date-time":"2014-10-30T05:01:31Z","timestamp":1414645291000},"page":"779-781","source":"Crossref","is-referenced-by-count":61,"title":["WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules"],"prefix":"10.1093","volume":"31","author":[{"given":"Michele","family":"Seeber","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angelo","family":"Felline","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Raimondi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simona","family":"Mariani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Fanelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,10,28]]},"reference":[{"key":"2023020116165663000_btu718-B1","doi-asserted-by":"crossref","first-page":"2504","DOI":"10.1021\/ct400096f","article-title":"A mixed protein structure network and elastic network model approach to predict the structural communication in biomolecular systems: the PDZ2 domain from tyrosine phosphatase 1E as a case study","volume":"9","author":"Raimondi","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"2023020116165663000_btu718-B2","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1002\/jcc.21688","article-title":"Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces","volume":"32","author":"Seeber","year":"2011","journal-title":"J. Comput. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/5\/779\/49011520\/bioinformatics_31_5_779.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/5\/779\/49011520\/bioinformatics_31_5_779.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:18:46Z","timestamp":1675297126000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/5\/779\/318084"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,28]]},"references-count":2,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2015,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu718","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2015,3]]},"published":{"date-parts":[[2014,10,28]]}}}