{"id":"https://openalex.org/W2116811279","doi":"https://doi.org/10.1371/journal.pcbi.1004461","title":"DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex\u2019s Dynamics","display_name":"DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex\u2019s Dynamics","publication_year":2015,"publication_date":"2015-10-27","ids":{"openalex":"https://openalex.org/W2116811279","doi":"https://doi.org/10.1371/journal.pcbi.1004461","mag":"2116811279","pmid":"https://pubmed.ncbi.nlm.nih.gov/26506003"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004461","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004461","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004461&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.1004461&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091551874","display_name":"Seren Soner","orcid":null},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Seren Soner","raw_affiliation_strings":["Department of Computer Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077817912","display_name":"Pemra \u00d6zbek","orcid":"https://orcid.org/0000-0002-3043-0015"},"institutions":[{"id":"https://openalex.org/I74897591","display_name":"Marmara University","ror":"https://ror.org/02kswqa67","country_code":"TR","type":"education","lineage":["https://openalex.org/I74897591"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Pemra Ozbek","raw_affiliation_strings":["Department of Bioengineering, Marmara University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Marmara University, Istanbul, Turkey","institution_ids":["https://openalex.org/I74897591"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005566175","display_name":"Jos\u00e9 Ignacio Garz\u00f3n","orcid":null},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose Ignacio Garzon","raw_affiliation_strings":["Departments of Biochemistry and Molecular Biophysics and Systems Biology and Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biochemistry and Molecular Biophysics and Systems Biology and Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037671858","display_name":"Nir Ben\u2010Tal","orcid":"https://orcid.org/0000-0001-6901-832X"},"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"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Nir Ben-Tal","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel","Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038256975","display_name":"T\u00fcrkan Halilo\u01e7lu","orcid":"https://orcid.org/0000-0002-1279-5803"},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Turkan Haliloglu","raw_affiliation_strings":["Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey","Department of Chemical Engineering and Polymer Research Center Bogazici University Istanbul Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Department of Chemical Engineering and Polymer Research Center Bogazici University Istanbul Turkey","institution_ids":["https://openalex.org/I4405392"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038256975"],"corresponding_institution_ids":["https://openalex.org/I4405392"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.3012,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.62205619,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"11","issue":"10","first_page":"e1004461","last_page":"e1004461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9941999912261963,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.6120212078094482},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"Protein dynamics","score":0.5522124171257019},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.47891557216644287},{"id":"https://openalex.org/keywords/hinge","display_name":"Hinge","score":0.45803430676460266},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.43233442306518555},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41681358218193054},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.368594765663147},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3595227003097534},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3209817409515381},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2214335799217224},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15912818908691406}],"concepts":[{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.6120212078094482},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.5522124171257019},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.47891557216644287},{"id":"https://openalex.org/C44000306","wikidata":"https://www.wikidata.org/wiki/Q244330","display_name":"Hinge","level":2,"score":0.45803430676460266},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.43233442306518555},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41681358218193054},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.368594765663147},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3595227003097534},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3209817409515381},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2214335799217224},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15912818908691406},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1004461","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004461","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004461&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:26506003","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26506003","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:3ff12170bc824125bfce94fcbdcfa0d3","is_oa":true,"landing_page_url":"https://doaj.org/article/3ff12170bc824125bfce94fcbdcfa0d3","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 11, Iss 10, p e1004461 (2015)","raw_type":"article"},{"id":"pmh:oai:dspace.marmara.edu.tr:11424/96151","is_oa":false,"landing_page_url":"https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=tsmetrics&SrcApp=tsm_test&DestApp=WOS_CPL&DestLinkType=FullRecord&KeyUT=ISI:000364399700030","pdf_url":null,"source":{"id":"https://openalex.org/S4306401380","display_name":"Dspace Repository (Marmara \u00dcniversitesi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74897591","host_organization_name":"Marmara University","host_organization_lineage":["https://openalex.org/I74897591"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:3610724","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4623975","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:figshare.com:article/1586090","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_DynaFace_Discrimination_between_Obligatory_and_Non_obligatory_Protein_Protein_Interactions_Based_on_the_Complex_8217_s_Dynamics_/1586090","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:openaccess.marmara.edu.tr:11424/245832","is_oa":true,"landing_page_url":"https://hdl.handle.net/11424/245832","pdf_url":null,"source":{"id":"https://openalex.org/S7407055305","display_name":"Marmara University Open Access System","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:openaccess.marmara.edu.tr:11424/96151","is_oa":true,"landing_page_url":"http://hdl.handle.net/11424/96151","pdf_url":null,"source":{"id":"https://openalex.org/S4306401380","display_name":"Dspace Repository (Marmara \u00dcniversitesi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I74897591","host_organization_name":"Marmara University","host_organization_lineage":["https://openalex.org/I74897591"],"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":"","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4623975","is_oa":true,"landing_page_url":"http://doi.org/10.1371/journal.pcbi.1004461","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":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004461","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004461","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004461&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":[{"score":0.5699999928474426,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"},{"score":0.4399999976158142,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G244242019","display_name":null,"funder_award_id":"1775/12","funder_id":"https://openalex.org/F4320335375","funder_display_name":"Planning and Budgeting Committee of the Council for Higher Education of Israel"},{"id":"https://openalex.org/G2776991352","display_name":null,"funder_award_id":"1775/12","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"},{"id":"https://openalex.org/G4284351861","display_name":null,"funder_award_id":"GM030518","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8702897804","display_name":null,"funder_award_id":"112T569","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335375","display_name":"Planning and Budgeting Committee of the Council for Higher Education of Israel","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116811279.pdf","grobid_xml":"https://content.openalex.org/works/W2116811279.grobid-xml"},"referenced_works_count":86,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1548387610","https://openalex.org/W1608369028","https://openalex.org/W1792865908","https://openalex.org/W1796728372","https://openalex.org/W1847469783","https://openalex.org/W1926568554","https://openalex.org/W1964083750","https://openalex.org/W1964850285","https://openalex.org/W1966907912","https://openalex.org/W1967408543","https://openalex.org/W1967974891","https://openalex.org/W1975107946","https://openalex.org/W1975449945","https://openalex.org/W1977845138","https://openalex.org/W1978237595","https://openalex.org/W1987749411","https://openalex.org/W1992806534","https://openalex.org/W1995924392","https://openalex.org/W2002870290","https://openalex.org/W2003079893","https://openalex.org/W2005386926","https://openalex.org/W2006424854","https://openalex.org/W2010022403","https://openalex.org/W2014286639","https://openalex.org/W2021213676","https://openalex.org/W2021904716","https://openalex.org/W2024138709","https://openalex.org/W2025639772","https://openalex.org/W2035503835","https://openalex.org/W2039473152","https://openalex.org/W2043699100","https://openalex.org/W2043809520","https://openalex.org/W2046241839","https://openalex.org/W2049934487","https://openalex.org/W2052475987","https://openalex.org/W2052637365","https://openalex.org/W2057813163","https://openalex.org/W2058017150","https://openalex.org/W2062048900","https://openalex.org/W2062185707","https://openalex.org/W2062414926","https://openalex.org/W2064791692","https://openalex.org/W2072157385","https://openalex.org/W2074826213","https://openalex.org/W2076058809","https://openalex.org/W2085277871","https://openalex.org/W2087918275","https://openalex.org/W2098416804","https://openalex.org/W2101017457","https://openalex.org/W2103105682","https://openalex.org/W2103210604","https://openalex.org/W2103485392","https://openalex.org/W2108700551","https://openalex.org/W2110440735","https://openalex.org/W2113024639","https://openalex.org/W2114306742","https://openalex.org/W2114886480","https://openalex.org/W2122071290","https://openalex.org/W2123482512","https://openalex.org/W2123583836","https://openalex.org/W2124013748","https://openalex.org/W2124036707","https://openalex.org/W2128276810","https://openalex.org/W2130479394","https://openalex.org/W2134971931","https://openalex.org/W2136832587","https://openalex.org/W2138458178","https://openalex.org/W2141627824","https://openalex.org/W2142796125","https://openalex.org/W2143047148","https://openalex.org/W2143881057","https://openalex.org/W2146672317","https://openalex.org/W2148219066","https://openalex.org/W2151311229","https://openalex.org/W2152281406","https://openalex.org/W2152444476","https://openalex.org/W2152521138","https://openalex.org/W2153153865","https://openalex.org/W2157035717","https://openalex.org/W2158100564","https://openalex.org/W2158156603","https://openalex.org/W2166496883","https://openalex.org/W2171017796","https://openalex.org/W4255308885","https://openalex.org/W4385126812"],"related_works":["https://openalex.org/W2092002011","https://openalex.org/W2914490533","https://openalex.org/W2945562222","https://openalex.org/W2027077329","https://openalex.org/W2378801510","https://openalex.org/W2010414728","https://openalex.org/W2290574198","https://openalex.org/W2021213676","https://openalex.org/W2946078915","https://openalex.org/W1970785155"],"abstract_inverted_index":{"Protein-protein":[0],"interfaces":[1],"have":[2],"been":[3],"evolutionarily-designed":[4],"to":[5,171],"enable":[6],"transduction":[7],"between":[8,100,108,120],"the":[9,18,21,27,30,42,46,55,62,77,81,94,98,106,109,116,133,142],"interacting":[10,95],"proteins.":[11],"Thus,":[12],"we":[13],"hypothesize":[14],"that":[15,60,135],"analysis":[16],"of":[17,20,29,45,80,87,132,149,155,180],"dynamics":[19],"complex":[22],"can":[23],"reveal":[24],"details":[25],"about":[26],"nature":[28],"interaction,":[31],"and":[32,66,97,153,174],"in":[33,70,113,141],"particular":[34],"whether":[35],"it":[36],"is":[37,186],"obligatory,":[38],"i.e.,":[39,76],"persists":[40],"throughout":[41],"entire":[43],"lifetime":[44],"proteins,":[47],"or":[48],"not.":[49],"Indeed,":[50],"normal":[51],"mode":[52],"analysis,":[53,147],"using":[54],"Gaussian":[56],"network":[57],"model,":[58],"shows":[59],"for":[61],"most":[63],"part":[64],"obligatory":[65,88,151,173],"non-obligatory":[67,114,157,175],"complexes":[68,89,115,159],"differ":[69],"their":[71,138],"decomposition":[72],"into":[73],"dynamic":[74,85,121],"domains,":[75,122],"mobile":[78],"elements":[79],"protein":[82,183],"complex.":[83],"The":[84],"domains":[86],"often":[90,118],"mix":[91],"segments":[92],"from":[93],"chains,":[96],"hinges":[99,119],"them":[101],"do":[102],"not":[103],"overlap":[104],"with":[105,137],"interface":[107,117,134],"chains.":[110],"In":[111,145],"contrast,":[112],"held":[123],"together":[124],"through":[125],"few":[126],"anchor":[127],"residues":[128],"on":[129],"one":[130],"side":[131],"interact":[136],"counterpart":[139],"grooves":[140],"other":[143],"end.":[144],"automatic":[146],"117":[148],"139":[150],"(84.2%)":[152],"203":[154],"246":[156],"(82.5%)":[158],"are":[160],"correctly":[161],"classified":[162],"by":[163],"our":[164],"method:":[165],"DynaFace.":[166],"We":[167],"further":[168],"use":[169],"DynaFace":[170,185],"predict":[172],"interactions":[176],"among":[177],"a":[178],"set":[179],"300":[181],"putative":[182],"complexes.":[184],"available":[187],"at:":[188],"http://safir.prc.boun.edu.tr/dynaface.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}