{"id":"https://openalex.org/W3163908429","doi":"https://doi.org/10.1093/nar/gkab350","title":"ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules","display_name":"ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules","publication_year":2021,"publication_date":"2021-04-22","ids":{"openalex":"https://openalex.org/W3163908429","doi":"https://doi.org/10.1093/nar/gkab350","mag":"3163908429","pmid":"https://pubmed.ncbi.nlm.nih.gov/33978752"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkab350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab350","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W551/38842270/gkab350.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/49/W1/W551/38842270/gkab350.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056449410","display_name":"Sophia F. Mersmann","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sophia\u00a0F Mersmann","raw_affiliation_strings":["Department of Mathematics, Imperial College London, Huxley Building, 180 Queen\u2019s Gate, London SW7 2AZ, UK","Department of Mathematics, Imperial College London, Huxley Building, 180 Queen's Gate, London SW7 2AZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Imperial College London, Huxley Building, 180 Queen\u2019s Gate, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Department of Mathematics, Imperial College London, Huxley Building, 180 Queen's Gate, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044490342","display_name":"L\u00e9onie Str\u00f6mich","orcid":"https://orcid.org/0000-0003-4498-813X"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"L\u00e9onie Str\u00f6mich","raw_affiliation_strings":["Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035342761","display_name":"Florian J Song","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Florian J Song","raw_affiliation_strings":["Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073671564","display_name":"Nan Wu","orcid":"https://orcid.org/0000-0003-4580-6019"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nan Wu","raw_affiliation_strings":["Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027144647","display_name":"Francesca Vianello","orcid":"https://orcid.org/0000-0002-3480-6294"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Francesca Vianello","raw_affiliation_strings":["Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058010593","display_name":"Mauricio Barahona","orcid":"https://orcid.org/0000-0002-1089-5675"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mauricio Barahona","raw_affiliation_strings":["Department of Mathematics, Imperial College London, Huxley Building, 180 Queen\u2019s Gate, London SW7 2AZ, UK","Department of Mathematics, Imperial College London, Huxley Building, 180 Queen's Gate, London SW7 2AZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Imperial College London, Huxley Building, 180 Queen\u2019s Gate, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Department of Mathematics, Imperial College London, Huxley Building, 180 Queen's Gate, London SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071259425","display_name":"Sophia N. Yaliraki","orcid":"https://orcid.org/0000-0002-8968-0713"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sophia\u00a0N Yaliraki","raw_affiliation_strings":["Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5071259425"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.7867,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.93906174,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"49","issue":"W1","first_page":"W551","last_page":"W558"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.8242232799530029},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.5785320997238159},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5625344514846802},{"id":"https://openalex.org/keywords/signalling","display_name":"Signalling","score":0.5159476399421692},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.49017268419265747},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46395888924598694},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4249420762062073},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4140406847000122},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.4131603538990021},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3389875292778015},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33208024501800537},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1940368115901947},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11529365181922913}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.8242232799530029},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.5785320997238159},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5625344514846802},{"id":"https://openalex.org/C39743133","wikidata":"https://www.wikidata.org/wiki/Q3262595","display_name":"Signalling","level":2,"score":0.5159476399421692},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.49017268419265747},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46395888924598694},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4249420762062073},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4140406847000122},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.4131603538990021},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3389875292778015},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33208024501800537},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1940368115901947},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11529365181922913},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005941","descriptor_name":"Glucokinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005941","descriptor_name":"Glucokinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005941","descriptor_name":"Glucokinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005941","descriptor_name":"Glucokinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkab350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab350","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W551/38842270/gkab350.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:33978752","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33978752","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:doi:10.6084/m9.figshare.12369125","is_oa":true,"landing_page_url":"https://iopscience.iop.org/article/10.1088/1478-3975/8/5/055010","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Online resource"},{"id":"pmh:oai:pubmedcentral.nih.gov:8661402","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8661402","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/89402","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/89402","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"W558","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkab350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkab350","pdf_url":"https://academic.oup.com/nar/article-pdf/49/W1/W551/38842270/gkab350.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1934935867","display_name":null,"funder_award_id":"Engineering and Physical Sciences R","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G2453345397","display_name":null,"funder_award_id":"EP/N014529/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4597177185","display_name":null,"funder_award_id":"Wellcome Trust","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6714377885","display_name":null,"funder_award_id":"215360/Z/19/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G7417950124","display_name":"EPSRC Centre for Mathematics of Precision Healthcare","funder_award_id":"EP/N014529/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8445413101","display_name":"EPSRC Centre for Doctoral Training in Physical Sciences Innovation in Chemical Biology for Bioindustry and Healthcare","funder_award_id":"EP/L015498/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G850745309","display_name":null,"funder_award_id":"EP/N014529/","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8895942654","display_name":null,"funder_award_id":"Imperial College","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320283","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3163908429.pdf","grobid_xml":"https://content.openalex.org/works/W3163908429.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W80438518","https://openalex.org/W1970294718","https://openalex.org/W1986795645","https://openalex.org/W2015807753","https://openalex.org/W2024912628","https://openalex.org/W2031149113","https://openalex.org/W2059087510","https://openalex.org/W2061463182","https://openalex.org/W2077912217","https://openalex.org/W2083975423","https://openalex.org/W2091226991","https://openalex.org/W2096904991","https://openalex.org/W2112040506","https://openalex.org/W2116993067","https://openalex.org/W2125299915","https://openalex.org/W2130479394","https://openalex.org/W2151794181","https://openalex.org/W2154249927","https://openalex.org/W2177124199","https://openalex.org/W2195592873","https://openalex.org/W2319108204","https://openalex.org/W2407736031","https://openalex.org/W2414667422","https://openalex.org/W2512708954","https://openalex.org/W2728165287","https://openalex.org/W2750148742","https://openalex.org/W2750485376","https://openalex.org/W2799327292","https://openalex.org/W2806399642","https://openalex.org/W2807983521","https://openalex.org/W2810801489","https://openalex.org/W2920104535","https://openalex.org/W2949703583","https://openalex.org/W2955268272","https://openalex.org/W2968728707","https://openalex.org/W2982347394","https://openalex.org/W3006316865","https://openalex.org/W3022823464","https://openalex.org/W3046878556","https://openalex.org/W3103789001","https://openalex.org/W3210534170","https://openalex.org/W4205482755","https://openalex.org/W4285682240","https://openalex.org/W6714135042","https://openalex.org/W6752829699","https://openalex.org/W6769161958","https://openalex.org/W6803339111"],"related_works":["https://openalex.org/W3113091479","https://openalex.org/W2162899405","https://openalex.org/W941090075","https://openalex.org/W2044987316","https://openalex.org/W3134374554","https://openalex.org/W2237480245","https://openalex.org/W2075065631","https://openalex.org/W2519167559","https://openalex.org/W4311248832","https://openalex.org/W4386113923"],"abstract_inverted_index":{"The":[0,122],"investigation":[1,35,148],"of":[2,9,36,49,63,66,75,107,110,116,149,154,160],"allosteric":[3,37,76,161],"effects":[4],"in":[5,13,151,168],"biomolecular":[6,54,152],"structures":[7,153],"is":[8,166],"great":[10],"current":[11],"interest":[12,155],"diverse":[14],"areas,":[15],"from":[16,45,113],"fundamental":[17],"biological":[18],"enquiry":[19],"to":[20,102,156,173],"drug":[21],"discovery.":[22],"Here":[23],"we":[24],"present":[25],"ProteinLens,":[26],"a":[27,50,53,72],"user-friendly":[28],"and":[29,69,78,90,95,99,105,134,163,170],"interactive":[30,132],"web":[31],"application":[32],"for":[33],"the":[34,46,64,67,81,103,108,119,147,158],"signalling":[38,77,150],"based":[39],"on":[40],"atomistic":[41],"graph-theoretical":[42],"methods.":[43],"Starting":[44],"PDB":[47],"file":[48],"biomolecule":[51],"(or":[52],"complex)":[55],"ProteinLens":[56,93,144,165],"obtains":[57],"an":[58],"atomistic,":[59],"energy-weighted":[60],"graph":[61],"description":[62],"structure":[65,82,137],"biomolecule,":[68],"subsequently":[70],"provides":[71],"systematic":[73],"analysis":[74],"communication":[79],"across":[80],"using":[83],"two":[84],"computationally":[85],"efficient":[86],"methods:":[87],"Markov":[88],"Transients":[89],"bond-to-bond":[91],"propensities.":[92],"scores":[94,129],"ranks":[96],"every":[97],"bond":[98],"residue":[100],"according":[101],"speed":[104],"magnitude":[106],"propagation":[109],"fluctuations":[111],"emanating":[112],"any":[114],"site":[115],"choice":[117],"(e.g.":[118],"active":[120],"site).":[121],"results":[123],"are":[124],"presented":[125],"through":[126],"statistical":[127],"quantile":[128],"visualised":[130],"with":[131],"plots":[133],"adjustable":[135],"3D":[136],"viewers,":[138],"which":[139],"can":[140],"also":[141],"be":[142],"downloaded.":[143],"thus":[145],"allows":[146],"aid":[157],"detection":[159],"sites":[162],"pathways.":[164],"implemented":[167],"Python/SQL":[169],"freely":[171],"available":[172],"use":[174],"at:":[175],"www.proteinlens.io.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
