{"id":"https://openalex.org/W2144477570","doi":"https://doi.org/10.1186/1471-2105-12-s1-s23","title":"Modeling allosteric signal propagation using protein structure networks","display_name":"Modeling allosteric signal propagation using protein structure networks","publication_year":2011,"publication_date":"2011-02-15","ids":{"openalex":"https://openalex.org/W2144477570","doi":"https://doi.org/10.1186/1471-2105-12-s1-s23","mag":"2144477570"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-s1-s23","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-s1-s23","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S1-S23","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S1-S23","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006597552","display_name":"Keunwan Park","orcid":"https://orcid.org/0000-0002-8783-9495"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I4210101891","display_name":"Korea Institute of Brain Science","ror":"https://ror.org/017stnw60","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210101891"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Keunwan Park","raw_affiliation_strings":["Department of Bio and Brain Engineering, KAIST, S Korea","Department of Bio and Brain Engineering, KAIST, S. Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bio and Brain Engineering, KAIST, S Korea","institution_ids":["https://openalex.org/I4210101891"]},{"raw_affiliation_string":"Department of Bio and Brain Engineering, KAIST, S. Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071721971","display_name":"Dongsup Kim","orcid":"https://orcid.org/0000-0002-5916-6799"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Dongsup Kim","raw_affiliation_strings":["Department of Bio and Brain Engineering, KAIST, S., Korea","Department of Bio and Brain Engineering, KAIST, S. Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bio and Brain Engineering, KAIST, S., Korea","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Department of Bio and Brain Engineering, KAIST, S. Korea","institution_ids":["https://openalex.org/I157485424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071721971"],"corresponding_institution_ids":["https://openalex.org/I157485424"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.5814,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.82901726,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"12","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9994000196456909,"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":0.9994000196456909,"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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9939000010490417,"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":0.9771803617477417},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5384523868560791},{"id":"https://openalex.org/keywords/radio-propagation","display_name":"Radio propagation","score":0.531889021396637},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.5290101170539856},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4575989842414856},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43432775139808655},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.419354647397995},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4110940098762512},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.398939847946167},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3606524169445038},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.35840243101119995},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19802767038345337},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.16069170832633972},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1234622597694397},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09555074572563171},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.08951479196548462}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.9771803617477417},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5384523868560791},{"id":"https://openalex.org/C202311505","wikidata":"https://www.wikidata.org/wiki/Q1474701","display_name":"Radio propagation","level":2,"score":0.531889021396637},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.5290101170539856},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4575989842414856},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43432775139808655},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.419354647397995},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4110940098762512},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.398939847946167},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3606524169445038},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.35840243101119995},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19802767038345337},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.16069170832633972},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1234622597694397},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09555074572563171},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.08951479196548462},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1471-2105-12-s1-s23","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-s1-s23","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S1-S23","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3044278","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3044278","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-s1-s23","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-s1-s23","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-S1-S23","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144477570.pdf","grobid_xml":"https://content.openalex.org/works/W2144477570.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1819481941","https://openalex.org/W1832993298","https://openalex.org/W1963570947","https://openalex.org/W1965611938","https://openalex.org/W1979511698","https://openalex.org/W1980274652","https://openalex.org/W1982874561","https://openalex.org/W1990374415","https://openalex.org/W1997291282","https://openalex.org/W2002302312","https://openalex.org/W2005474992","https://openalex.org/W2009123297","https://openalex.org/W2017428798","https://openalex.org/W2018262140","https://openalex.org/W2028645925","https://openalex.org/W2033893117","https://openalex.org/W2040078255","https://openalex.org/W2045001436","https://openalex.org/W2049598343","https://openalex.org/W2049682677","https://openalex.org/W2062575219","https://openalex.org/W2062762346","https://openalex.org/W2068705129","https://openalex.org/W2073690777","https://openalex.org/W2075379212","https://openalex.org/W2083975423","https://openalex.org/W2088311925","https://openalex.org/W2089189332","https://openalex.org/W2091060891","https://openalex.org/W2092006899","https://openalex.org/W2093397531","https://openalex.org/W2094571158","https://openalex.org/W2096165020","https://openalex.org/W2097164795","https://openalex.org/W2103578846","https://openalex.org/W2124676068","https://openalex.org/W2127387319","https://openalex.org/W2133521217","https://openalex.org/W2134742468","https://openalex.org/W2137714679","https://openalex.org/W2140820106","https://openalex.org/W2156232082","https://openalex.org/W2160329145","https://openalex.org/W2963217003","https://openalex.org/W3103453712","https://openalex.org/W3141829038"],"related_works":["https://openalex.org/W2046450796","https://openalex.org/W2939998722","https://openalex.org/W2169750653","https://openalex.org/W2195592873","https://openalex.org/W1971782741","https://openalex.org/W3005062988","https://openalex.org/W4211217675","https://openalex.org/W2911329269","https://openalex.org/W2075777827","https://openalex.org/W2051337563"],"abstract_inverted_index":{"Allosteric":[0],"communication":[1,185],"in":[2,134,167,182],"proteins":[3],"can":[4],"be":[5],"induced":[6],"by":[7,41,59,102,115],"the":[8,23,35,42,53,80,84,90,104,111,125,149,164],"binding":[9,169],"of":[10,151,157],"effective":[11],"ligands,":[12],"mutations":[13],"or":[14],"covalent":[15],"modifications":[16],"that":[17,38,124,163,178],"regulate":[18],"a":[19,61,70,76,95],"site":[20,99],"distant":[21],"from":[22,94],"perturbed":[24],"region.":[25],"To":[26],"understand":[27],"allosteric":[28,48,135],"regulation,":[29],"it":[30],"is":[31],"important":[32,132],"to":[33,78,141],"identify":[34],"remote":[36],"sites":[37],"are":[39,50],"affected":[40],"perturbation-induced":[43],"signals":[44],"and":[45,65,83,147],"how":[46],"these":[47],"perturbations":[49],"transmitted":[51],"within":[52],"protein":[54,62,143,168,187],"structure.":[55],"In":[56,87],"this":[57],"study,":[58],"constructing":[60],"structure":[63],"network":[64],"modeling":[66],"signal":[67,81,97,116,184],"transmission":[68,117],"with":[69,127],"Markov":[71],"random":[72],"walk,":[73],"we":[74],"developed":[75],"method":[77],"estimate":[79],"propagation":[82],"resulting":[85],"effects.":[86],"our":[88,139,152],"model,":[89],"global":[91],"perturbation":[92],"effects":[93,113],"particular":[96],"initiation":[98],"were":[100],"estimated":[101],"calculating":[103],"expected":[105],"visiting":[106],"time":[107],"(EVT),":[108],"which":[109,176],"describes":[110],"signal-induced":[112],"caused":[114],"through":[118],"all":[119],"possible":[120],"routes.":[121],"We":[122,137,160],"hypothesized":[123],"residues":[126],"high":[128,173],"EVT":[129,174],"values":[130],"play":[131,180],"roles":[133,181],"signaling.":[136],"applied":[138],"model":[140,153],"two":[142],"structures":[144],"as":[145],"examples,":[146],"verified":[148],"validity":[150],"using":[154],"various":[155],"types":[156],"experimental":[158],"data.":[159],"also":[161],"found":[162],"hot":[165],"spots":[166],"interfaces":[170],"have":[171],"significantly":[172],"values,":[175],"suggests":[177],"they":[179],"mediating":[183],"between":[186],"domains.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
