{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T01:32:55Z","timestamp":1775611975755,"version":"3.50.1"},"reference-count":98,"publisher":"American Chemical Society (ACS)","issue":"14","license":[{"start":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T00:00:00Z","timestamp":1689120000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T00:00:00Z","timestamp":1689120000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T00:00:00Z","timestamp":1689120000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001732","name":"Danmarks Grundforskningsfond","doi-asserted-by":"publisher","award":["DNRF125"],"award-info":[{"award-number":["DNRF125"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012331","name":"LEO Fondet","doi-asserted-by":"publisher","award":["LF17006"],"award-info":[{"award-number":["LF17006"]}],"id":[{"id":"10.13039\/501100012331","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Fonden","doi-asserted-by":"publisher","award":["26802"],"award-info":[{"award-number":["26802"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009910","name":"Hartmann Fonden","doi-asserted-by":"publisher","award":["R421-A33877"],"award-info":[{"award-number":["R421-A33877"]}],"id":[{"id":"10.13039\/501100009910","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002808","name":"Carlsbergfondet","doi-asserted-by":"publisher","award":["CF18-0314"],"award-info":[{"award-number":["CF18-0314"]}],"id":[{"id":"10.13039\/501100002808","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Biotechnology-based Synthesis and Production","award":["17OC0027588"],"award-info":[{"award-number":["17OC0027588"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2023,7,24]]},"DOI":"10.1021\/acs.jcim.3c00574","type":"journal-article","created":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T14:45:11Z","timestamp":1689173111000},"page":"4237-4245","source":"Crossref","is-referenced-by-count":24,"title":["PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles"],"prefix":"10.1021","volume":"63","author":[{"given":"Valentina","family":"Sora","sequence":"first","affiliation":[{"name":"Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark"},{"name":"Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark"}]},{"given":"Matteo","family":"Tiberti","sequence":"additional","affiliation":[{"name":"Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3855-1417","authenticated-orcid":true,"given":"Ludovica","family":"Beltrame","sequence":"additional","affiliation":[{"name":"Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3427-3205","authenticated-orcid":true,"given":"Deniz","family":"Dogan","sequence":"additional","affiliation":[{"name":"Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark"}]},{"given":"Shahriyar Mahdi","family":"Robbani","sequence":"additional","affiliation":[{"name":"Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark"}]},{"given":"Joshua","family":"Rubin","sequence":"additional","affiliation":[{"name":"Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7376-5894","authenticated-orcid":true,"given":"Elena","family":"Papaleo","sequence":"additional","affiliation":[{"name":"Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark"},{"name":"Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark"}]}],"member":"316","published-online":{"date-parts":[[2023,7,12]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1038\/nature13001"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2018.09.004"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2018.10.008"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz093"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1021\/ct500536r"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2009.06.008"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003394"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2015.00028"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.5b00623"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.5b00543"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.5b00541"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3324"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004507"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1120536109"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1502"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0810961106"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1021\/cr3002356"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2015.03.001"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2015.02.015"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1021\/ct4008603"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(04)74086-2"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.65.061910"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003744"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1002\/pro.711"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac365"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2020.06.006"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.04.463034"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1061"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2018.08.011"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035686"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003207"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-010-0519-z"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0704459104"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbagen.2019.07.008"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2016.00078"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0506-8"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1491"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00206"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1038\/nm.4089"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13803-0"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1507"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006701"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007665"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1021\/ci400639r"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007485"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddv370"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006458"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1039\/C6RA06312H"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1093\/rheumatology\/keaa269"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21176264"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2020.144561"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1042\/BCJ20200799"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1038\/s41418-021-00766-3"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1016\/j.crstbi.2021.11.002"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-71527-4"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1080\/15548627.2020.1847443"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2014.08.011"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2014.09.018"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0169586"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2016.07.003"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-016-9978-0"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-05722-3"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1016\/j.bcp.2020.113869"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw770"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1038\/srep34277"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.3389\/fnmol.2019.00050"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-37367-z"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.9b00846"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.3390\/biom10101408"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20205009"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22158318"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.0c11562"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1016\/j.sapharm.2020.10.007"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2022.167663"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000470"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-374"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-01498-6"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.105.064485"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.25080\/majora-629e541a-00e"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21787"},{"key":"ref81\/cit81","doi-asserted-by":"crossref","unstructured":"Hagberg, A. A.; Schult, D. A.; Swart, P. J. Exploring Network Structure, Dynamics, and Function Using NetworkX. In\n                      7th Python in Science Conference (SciPy 2008)\n                      , 2008; pp 11\u201315.","DOI":"10.25080\/TCWV9851"},{"key":"ref82\/cit82","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-408143-7.00003-7"},{"key":"ref83\/cit83","doi-asserted-by":"publisher","DOI":"10.25080\/majora-7b98e3ed-013"},{"key":"ref84\/cit84","doi-asserted-by":"publisher","DOI":"10.2174\/1389203716666150923105727"},{"key":"ref85\/cit85","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21688"},{"key":"ref86\/cit86","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky381"},{"key":"ref87\/cit87","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz399"},{"key":"ref88\/cit88","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx349"},{"key":"ref89\/cit89","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3923"},{"key":"ref90\/cit90","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5998"},{"key":"ref91\/cit91","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2592"},{"key":"ref92\/cit92","doi-asserted-by":"publisher","DOI":"10.1038\/nature08615"},{"key":"ref93\/cit93","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1404220111"},{"key":"ref94\/cit94","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2012.11.3815"},{"key":"ref95\/cit95","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-019-0136-1"},{"key":"ref96\/cit96","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2022.864874"},{"key":"ref97\/cit97","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.06.069"},{"key":"ref98\/cit98","doi-asserted-by":"publisher","DOI":"10.1101\/2022.02.07.479254"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.3c00574","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.3c00574","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T21:12:46Z","timestamp":1729717966000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.3c00574"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,12]]},"references-count":98,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2023,7,24]]}},"alternative-id":["10.1021\/acs.jcim.3c00574"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.3c00574","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.11.22.381616","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,12]]}}}