{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T18:37:28Z","timestamp":1773167848904,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T00:00:00Z","timestamp":1620777600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/N014529\/1"],"award-info":[{"award-number":["EP\/N014529\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/L015498\/1"],"award-info":[{"award-number":["EP\/L015498\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["215360\/Z\/19\/Z"],"award-info":[{"award-number":["215360\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000761","name":"Imperial College London","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000761","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The investigation of allosteric effects in biomolecular structures is of great current interest in diverse areas, from fundamental biological enquiry to drug discovery. Here we present ProteinLens, a user-friendly and interactive web application for the investigation of allosteric signalling based on atomistic graph-theoretical methods. Starting from the PDB file of a biomolecule (or a biomolecular complex) ProteinLens obtains an atomistic, energy-weighted graph description of the structure of the biomolecule, and subsequently provides a systematic analysis of allosteric signalling and communication across the structure using two computationally efficient methods: Markov Transients and bond-to-bond propensities. ProteinLens scores and ranks every bond and residue according to the speed and magnitude of the propagation of fluctuations emanating from any site of choice (e.g.\u00a0the active site). The results are presented through statistical quantile scores visualised with interactive plots and adjustable 3D structure viewers, which can also be downloaded. ProteinLens thus allows the investigation of signalling in biomolecular structures of interest to aid the detection of allosteric sites and pathways. ProteinLens is implemented in Python\/SQL and freely available to use at: www.proteinlens.io.<\/jats:p>","DOI":"10.1093\/nar\/gkab350","type":"journal-article","created":{"date-parts":[[2021,4,22]],"date-time":"2021-04-22T23:39:28Z","timestamp":1619134768000},"page":"W551-W558","source":"Crossref","is-referenced-by-count":30,"title":["ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules"],"prefix":"10.1093","volume":"49","author":[{"given":"Sophia\u00a0F","family":"Mersmann","sequence":"first","affiliation":[{"name":"Department of Mathematics, Imperial College London, Huxley Building, 180 Queen\u2019s Gate, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L\u00e9onie","family":"Str\u00f6mich","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian J","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nan","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Vianello","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mauricio","family":"Barahona","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Imperial College London, Huxley Building, 180 Queen\u2019s Gate, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8968-0713","authenticated-orcid":false,"given":"Sophia\u00a0N","family":"Yaliraki","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,5,12]]},"reference":[{"key":"2021070812061587900_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.sbi.2015.10.004","article-title":"Allosteric sites: remote control in regulation of protein activity","volume":"37","author":"Guarnera","year":"2016","journal-title":"Curr. 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