{"id":"https://openalex.org/W2146099270","doi":"https://doi.org/10.1371/journal.pcbi.1000975","title":"Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks","display_name":"Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks","publication_year":2010,"publication_date":"2010-11-04","ids":{"openalex":"https://openalex.org/W2146099270","doi":"https://doi.org/10.1371/journal.pcbi.1000975","mag":"2146099270","pmid":"https://pubmed.ncbi.nlm.nih.gov/21079669"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000975","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000975","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000975&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000975&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054779204","display_name":"Julien F. Ollivier","orcid":null},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["CA","GB"],"is_corresponding":true,"raw_author_name":"Julien F. Ollivier","raw_affiliation_strings":["Department of Physiology, McGill University, Centre for Nonlinear Dynamics, Montreal, Qu\u00e9bec, Canada. julien.ollivier@gmail.com","Centre for Nonlinear Dynamics, Department of Physiology, McGill University, Montreal, Qu\u00e9bec, Canada","Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology, McGill University, Centre for Nonlinear Dynamics, Montreal, Qu\u00e9bec, Canada. julien.ollivier@gmail.com","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Centre for Nonlinear Dynamics, Department of Physiology, McGill University, Montreal, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052845258","display_name":"Vahid Shahrezaei","orcid":"https://orcid.org/0000-0002-4013-5458"},"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":"Vahid Shahrezaei","raw_affiliation_strings":["Department of Mathematics, Imperial College London, London, United Kingdom","Department of Mathematics Imperial College London London United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Department of Mathematics Imperial College London London United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053098071","display_name":"Peter S. Swain","orcid":"https://orcid.org/0000-0001-7489-8587"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Peter S. Swain","raw_affiliation_strings":["Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053098071","https://openalex.org/A5054779204"],"corresponding_institution_ids":["https://openalex.org/I5023651","https://openalex.org/I98677209"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.7433,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.84167086,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"11","first_page":"e1000975","last_page":"e1000975"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9994999766349792,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"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":0.9975000023841858,"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":0.9433237910270691},{"id":"https://openalex.org/keywords/cooperativity","display_name":"Cooperativity","score":0.7614918947219849},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.6201733350753784},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5972108244895935},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.5607286095619202},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5038086771965027},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.4773402512073517},{"id":"https://openalex.org/keywords/allosteric-enzyme","display_name":"Allosteric enzyme","score":0.45593661069869995},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.45408207178115845},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4266355633735657},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3022615313529968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.284404993057251},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.13683044910430908},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13464340567588806}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.9433237910270691},{"id":"https://openalex.org/C166014724","wikidata":"https://www.wikidata.org/wiki/Q337217","display_name":"Cooperativity","level":2,"score":0.7614918947219849},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.6201733350753784},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5972108244895935},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.5607286095619202},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5038086771965027},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.4773402512073517},{"id":"https://openalex.org/C109964505","wikidata":"https://www.wikidata.org/wiki/Q3321436","display_name":"Allosteric enzyme","level":4,"score":0.45593661069869995},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.45408207178115845},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4266355633735657},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3022615313529968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.284404993057251},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.13683044910430908},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13464340567588806},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D001667","descriptor_name":"Binding, Competitive","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001667","descriptor_name":"Binding, Competitive","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001667","descriptor_name":"Binding, Competitive","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D043562","descriptor_name":"Receptors, G-Protein-Coupled","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1000975","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000975","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000975&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:21079669","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21079669","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:europepmc.org:2025727","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2973810","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.349.2210","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.349.2210","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/f4/dc/PLoS_Comput_Biol_2010_Nov_4_6(11)_e1000975.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:6cb68f305e13429885e5414b4864b9c4","is_oa":true,"landing_page_url":"https://doaj.org/article/6cb68f305e13429885e5414b4864b9c4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 6, Iss 11, p e1000975 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/140771","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Scalable_Rule_Based_Modelling_of_Allosteric_Proteins_and_Biochemical_Networks/140771","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/ed757cc6-79c8-4600-b4c0-5986f5e26dec","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/ed757cc6-79c8-4600-b4c0-5986f5e26dec","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Ollivier, J F, Shahrezaei, V & Swain, P S 2010, 'Scalable rule-based modelling of allosteric proteins and biochemical networks', PLoS Computational Biology, vol. 6, no. 11, e1000975. https://doi.org/10.1371/journal.pcbi.1000975","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/ed757cc6-79c8-4600-b4c0-5986f5e26dec","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11820/ed757cc6-79c8-4600-b4c0-5986f5e26dec","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pure.ed.ac.uk:publications/ed757cc6-79c8-4600-b4c0-5986f5e26dec","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11820/ed757cc6-79c8-4600-b4c0-5986f5e26dec","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Ollivier, J F, Shahrezaei, V & Swain, P S 2010, 'Scalable rule-based modelling of allosteric proteins and biochemical networks', PLoS Computational Biology, vol. 6, no. 11, e1000975. https://doi.org/10.1371/journal.pcbi.1000975","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000975","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000975","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000975&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321747","display_name":"Fonds Qu\u00e9b\u00e9cois de la Recherche sur la Nature et les Technologies","ror":"https://ror.org/00b9f9778"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146099270.pdf","grobid_xml":"https://content.openalex.org/works/W2146099270.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1491768362","https://openalex.org/W1598181139","https://openalex.org/W1599936794","https://openalex.org/W1603274157","https://openalex.org/W1632324362","https://openalex.org/W1644749979","https://openalex.org/W1660272337","https://openalex.org/W1966101832","https://openalex.org/W1975845571","https://openalex.org/W1977290213","https://openalex.org/W1977943300","https://openalex.org/W1982186905","https://openalex.org/W1986649132","https://openalex.org/W1987030497","https://openalex.org/W1990461661","https://openalex.org/W1998093640","https://openalex.org/W2000782090","https://openalex.org/W2005392755","https://openalex.org/W2005524843","https://openalex.org/W2005749181","https://openalex.org/W2005977960","https://openalex.org/W2009915001","https://openalex.org/W2009955424","https://openalex.org/W2014826286","https://openalex.org/W2015117663","https://openalex.org/W2016940132","https://openalex.org/W2019074781","https://openalex.org/W2021209514","https://openalex.org/W2025476423","https://openalex.org/W2026804158","https://openalex.org/W2032790231","https://openalex.org/W2033406586","https://openalex.org/W2034492556","https://openalex.org/W2040860090","https://openalex.org/W2040896718","https://openalex.org/W2053004995","https://openalex.org/W2055512632","https://openalex.org/W2061425021","https://openalex.org/W2063366436","https://openalex.org/W2064746296","https://openalex.org/W2065174436","https://openalex.org/W2069941324","https://openalex.org/W2075260598","https://openalex.org/W2075345465","https://openalex.org/W2081128554","https://openalex.org/W2087234479","https://openalex.org/W2091742123","https://openalex.org/W2094590111","https://openalex.org/W2095775529","https://openalex.org/W2097036312","https://openalex.org/W2099693848","https://openalex.org/W2106362845","https://openalex.org/W2111682035","https://openalex.org/W2116695133","https://openalex.org/W2122284068","https://openalex.org/W2129788952","https://openalex.org/W2132033525","https://openalex.org/W2136672278","https://openalex.org/W2136943420","https://openalex.org/W2145080853","https://openalex.org/W2150908245","https://openalex.org/W2152223517","https://openalex.org/W2157245081","https://openalex.org/W2161406501","https://openalex.org/W2163493106","https://openalex.org/W2165714871","https://openalex.org/W2168281812","https://openalex.org/W2169193349","https://openalex.org/W2172021704","https://openalex.org/W2172659222","https://openalex.org/W2336542886","https://openalex.org/W4294604981","https://openalex.org/W4298752002","https://openalex.org/W6635732319"],"related_works":["https://openalex.org/W2752794680","https://openalex.org/W2747094833","https://openalex.org/W4327936846","https://openalex.org/W4319874929","https://openalex.org/W2572355597","https://openalex.org/W1982170406","https://openalex.org/W4244005486","https://openalex.org/W1971229210","https://openalex.org/W2117032992","https://openalex.org/W2108651323"],"abstract_inverted_index":{"Much":[0],"of":[1,4,12,34,50,60,72,87,116,128,143,163,188,198,212,214,232],"the":[2,9,48,58,67,84,114,126,140,160,185,209],"complexity":[3],"biochemical":[5,73,233],"networks":[6,234],"comes":[7],"from":[8],"information-processing":[10],"abilities":[11],"allosteric":[13,25,117,190],"proteins,":[14],"be":[15,28],"they":[16],"receptors,":[17],"ion-channels,":[18],"signalling":[19],"molecules":[20,36],"or":[21],"transcription":[22],"factors.":[23],"An":[24],"protein":[26,61,88],"can":[27,175,183,207],"uniquely":[29],"regulated":[30],"by":[31],"each":[32],"combination":[33],"input":[35],"that":[37,82,202],"it":[38],"binds.":[39],"This":[40],"\"regulatory":[41],"complexity\"":[42],"causes":[43],"a":[44,78,144,195,218,224],"combinatorial":[45],"increase":[46],"in":[47,235],"number":[49,59,127],"parameters":[51,129],"required":[52,130],"to":[53,90,131,171],"fit":[54,132],"experimental":[55],"data":[56],"as":[57,98,107],"interactions":[62],"increases.":[63],"It":[64],"therefore":[65],"challenges":[66],"creation,":[68],"updating,":[69],"and":[70,134,138,154,159,179,206,229,237],"re-use":[71],"models.":[74],"Here,":[75],"we":[76,101,123],"propose":[77],"rule-based":[79],"modelling":[80,113,231],"framework":[81],"exploits":[83],"intrinsic":[85],"modularity":[86],"structure":[89,105],"address":[91],"regulatory":[92],"complexity.":[93],"Rather":[94],"than":[95],"treating":[96],"proteins":[97,118],"\"black":[99],"boxes\",":[100],"model":[102,197],"their":[103],"hierarchical":[104],"and,":[106],"conformational":[108,121],"changes,":[109,122],"internal":[110],"dynamics.":[111],"By":[112],"regulation":[115],"through":[119,217],"these":[120],"often":[124],"decrease":[125],"data,":[133],"so":[135],"reduce":[136],"over-fitting":[137],"improve":[139],"predictive":[141],"power":[142],"model.":[145],"Our":[146,220],"method":[147],"is":[148],"thermodynamically":[149],"grounded,":[150],"imposes":[151],"detailed":[152],"balance,":[153],"also":[155,193],"includes":[156],"molecular":[157],"cross-talk":[158],"background":[161],"activity":[162],"enzymes.":[164],"We":[165,192],"use":[166],"our":[167],"Allosteric":[168],"Network":[169],"Compiler":[170],"examine":[172],"how":[173,180],"allostery":[174],"facilitate":[176],"macromolecular":[177],"assembly":[178],"competitive":[181],"ligands":[182],"change":[184],"observed":[186],"cooperativity":[187],"an":[189],"protein.":[191],"develop":[194],"parsimonious":[196],"G":[199],"protein-coupled":[200],"receptors":[201],"explains":[203],"functional":[204],"selectivity":[205],"predict":[208],"rank":[210],"order":[211],"potency":[213],"agonists":[215],"acting":[216],"receptor.":[219],"methodology":[221],"should":[222],"provide":[223],"basis":[225],"for":[226],"scalable,":[227],"modular":[228],"executable":[230],"systems":[236],"synthetic":[238],"biology.":[239]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-12T21:12:35.861297","created_date":"2025-10-10T00:00:00"}
