{"id":"https://openalex.org/W2577454214","doi":"https://doi.org/10.1371/journal.pcbi.1005290","title":"Computing the Dynamic Supramolecular Structural Proteome","display_name":"Computing the Dynamic Supramolecular Structural Proteome","publication_year":2017,"publication_date":"2017-01-19","ids":{"openalex":"https://openalex.org/W2577454214","doi":"https://doi.org/10.1371/journal.pcbi.1005290","mag":"2577454214","pmid":"https://pubmed.ncbi.nlm.nih.gov/28103234"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005290","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005290","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005290&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":"editorial","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.1005290&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025357844","display_name":"Ruth Nussinov","orcid":"https://orcid.org/0000-0002-8115-6415"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I114662689","display_name":"Leidos (United States)","ror":"https://ror.org/012cvds63","country_code":"US","type":"company","lineage":["https://openalex.org/I114662689"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Ruth Nussinov","raw_affiliation_strings":["Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America","Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America","institution_ids":["https://openalex.org/I114662689","https://openalex.org/I4210140884","https://openalex.org/I4210130649"]},{"raw_affiliation_string":"Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["University of Virginia, Charlottesville, Virginia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013394507","display_name":"Ilya A. Vakser","orcid":"https://orcid.org/0000-0002-5743-2934"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ilya Vakser","raw_affiliation_strings":["Center for Computational Biology, The University of Kansas, Lawrence, Kansas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, Kansas, United States of America","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025357844"],"corresponding_institution_ids":["https://openalex.org/I114662689","https://openalex.org/I16391192","https://openalex.org/I4210130649","https://openalex.org/I4210140884"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.3365,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.58761025,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"13","issue":"1","first_page":"e1005290","last_page":"e1005290"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9970999956130981,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9970999956130981,"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":0.9959999918937683,"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":0.9948999881744385,"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/proteome","display_name":"Proteome","score":0.6281684041023254},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5879461169242859},{"id":"https://openalex.org/keywords/supramolecular-chemistry","display_name":"Supramolecular chemistry","score":0.48469069600105286},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42781826853752136},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3263513147830963},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3226218521595001},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.29962947964668274},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.09788048267364502}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6281684041023254},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5879461169242859},{"id":"https://openalex.org/C93275456","wikidata":"https://www.wikidata.org/wiki/Q756449","display_name":"Supramolecular chemistry","level":3,"score":0.48469069600105286},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42781826853752136},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3263513147830963},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3226218521595001},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29962947964668274},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.09788048267364502},{"id":"https://openalex.org/C115624301","wikidata":"https://www.wikidata.org/wiki/Q895901","display_name":"Crystal structure","level":2,"score":0.0}],"mesh":[{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1005290","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005290","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005290&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:28103234","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28103234","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:doaj.org/article:eee542aa191e4d98bbd1f4300b7d5363","is_oa":true,"landing_page_url":"https://doaj.org/article/eee542aa191e4d98bbd1f4300b7d5363","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 13, Iss 1, p e1005290 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4154885","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5245783","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:kuscholarworks.ku.edu:1808/27382","is_oa":true,"landing_page_url":"http://hdl.handle.net/1808/27382","pdf_url":null,"source":{"id":"https://openalex.org/S4306400421","display_name":"KU ScholarWorks (The University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005290","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005290","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005290&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":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2577454214.pdf","grobid_xml":"https://content.openalex.org/works/W2577454214.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1965907701","https://openalex.org/W2000383223","https://openalex.org/W2022284509","https://openalex.org/W2024911966","https://openalex.org/W2032402250","https://openalex.org/W2038678667","https://openalex.org/W2054113335","https://openalex.org/W2067455153","https://openalex.org/W2152444476","https://openalex.org/W2153983456","https://openalex.org/W2158071704","https://openalex.org/W2473226680","https://openalex.org/W2554019130","https://openalex.org/W2554109484","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2316833920","https://openalex.org/W4377098514","https://openalex.org/W4387564043","https://openalex.org/W2290118617","https://openalex.org/W1975345997","https://openalex.org/W2019197244","https://openalex.org/W2132744522","https://openalex.org/W2048777227","https://openalex.org/W2967223254","https://openalex.org/W2054792938"],"abstract_inverted_index":{"Cells":[0],"execute":[1],"their":[2],"functions":[3,38],"through":[4,97,104],"protein":[5],"interactions.":[6],"The":[7,133],"pathways":[8],"they":[9,28,50,53,64],"link":[10],"are":[11,25,39,51,58,65],"neither":[12],"discrete":[13],"nor":[14],"spatially":[15],"separated,":[16],"as":[17],"typically":[18],"depicted":[19],"in":[20,68,127],"cellular":[21,145],"diagrams.":[22],"Cellular":[23],"diagrams":[24],"useful;":[26],"however,":[27],"neglect":[29],"the":[30,69,77,84,114,117,126,136,143],"physical":[31,130],"structure":[32],"of":[33,55,116,135],"cell":[34,91,131],"signaling.":[35],"In":[36],"reality,":[37],"shaped":[40],"by":[41],"molecular":[42],"transitions":[43],"between":[44],"small-and":[45],"large-supramolecular":[46],"assemblies.":[47],"Even":[48],"though":[49],"preorganized,":[52],"consist":[54],"clusters":[56],"that":[57,147],"loose":[59],"and":[60,71,76,89,99,139],"dynamic.":[61],"Importantly":[62],"too,":[63],"often":[66],"anchored":[67],"membrane":[70],"interact":[72],"with":[73],"scaffolding":[74],"proteins":[75],"cytoskeleton.":[78],"Their":[79],"continuum":[80],"may":[81],"physically":[82],"span":[83],"cell.":[85],"Indeed,":[86],"efficient,":[87],"productive,":[88],"reliable":[90],"signaling":[92],"can":[93],"only":[94,155],"take":[95],"place":[96],"transient":[98],"cooperative":[100],"protein-protein":[101],"interactions,":[102],"not":[103,122],"stochastic,":[105],"diffusion-controlled":[106],"processes.":[107],"Despite":[108],"this,":[109],"current":[110],"computational":[111],"approaches":[112],"to":[113,157],"modeling":[115],"structural":[118],"proteome":[119],"still":[120],"do":[121],"fully":[123],"account":[124],"for":[125],"vivo,":[128],"real":[129],"organization.":[132],"enigmas":[134],"assembly":[137],"sizes":[138],"dynamic":[140],"conformational":[141],"distributions-and":[142],"diverse":[144],"environments":[146],"influence":[148],"thempresent":[149],"daunting":[150],"challenges,":[151],"which":[152],"we":[153],"have":[154],"begun":[156],"address.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-14T08:36:36.166977","created_date":"2025-10-10T00:00:00"}