{"id":"https://openalex.org/W2967720048","doi":"https://doi.org/10.1109/cibcb.2019.8791469","title":"A Probabilistic Programming Approach to Protein Structure Superposition","display_name":"A Probabilistic Programming Approach to Protein Structure Superposition","publication_year":2019,"publication_date":"2019-07-01","ids":{"openalex":"https://openalex.org/W2967720048","doi":"https://doi.org/10.1109/cibcb.2019.8791469","mag":"2967720048","pmid":"https://pubmed.ncbi.nlm.nih.gov/34661202"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2019.8791469","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2019.8791469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8515897","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045539629","display_name":"Lys Sanz Moreta","orcid":"https://orcid.org/0000-0003-1580-539X"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Lys Sanz Moreta","raw_affiliation_strings":["Department of Computer Science. University of Copenhagen, Denmark","Department of Computer Science, University of Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science. University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Department of Computer Science, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065468895","display_name":"Ahmad Salim Al-Sibahi","orcid":"https://orcid.org/0000-0002-3445-2334"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Ahmad Salim Al-Sibahi","raw_affiliation_strings":["Department of Computer Science. University of Copenhagen/Skanned.com, Denmark","Department of Computer Science, University of Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science. University of Copenhagen/Skanned.com, Denmark","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046700536","display_name":"Douglas L. Theobald","orcid":"https://orcid.org/0000-0002-2695-8343"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas Theobald","raw_affiliation_strings":["Department of Biochemistry. Brandeis University. Waltham, MA 02452, USA","Department of Biochemistry, Brandeis University, Waltham, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry. Brandeis University. Waltham, MA 02452, USA","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"Department of Biochemistry, Brandeis University, Waltham, MA, USA","institution_ids":["https://openalex.org/I6902469"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086977430","display_name":"William C. Bullock","orcid":null},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"William Bullock","raw_affiliation_strings":["The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","The Bioinformatics Centre, University of Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","institution_ids":[]},{"raw_affiliation_string":"The Bioinformatics Centre, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064981996","display_name":"Basile Rommes","orcid":"https://orcid.org/0000-0001-6755-6503"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Basile Nicolas Rommes","raw_affiliation_strings":["The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","The Bioinformatics Centre, University of Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","institution_ids":[]},{"raw_affiliation_string":"The Bioinformatics Centre, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032867518","display_name":"Andreas Manoukian","orcid":null},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Andreas Manoukian","raw_affiliation_strings":["The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","The Bioinformatics Centre, University of Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","institution_ids":[]},{"raw_affiliation_string":"The Bioinformatics Centre, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047821550","display_name":"Thomas Hamelryck","orcid":"https://orcid.org/0000-0003-2917-3602"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Thomas Hamelryck","raw_affiliation_strings":["Department of Computer Science. University of Copenhagen, Denmark","The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","The Bioinformatics Centre, University of Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science. University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"The Bioinformatics Centre. Section for Computational and RNA Biology. University of Copenhagen. Copenhagen, Denmark","institution_ids":[]},{"raw_affiliation_string":"The Bioinformatics Centre, University of Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5045539629"],"corresponding_institution_ids":["https://openalex.org/I124055696"],"apc_list":null,"apc_paid":null,"fwci":0.0856,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.47430977,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"12","issue":null,"first_page":"1","last_page":"5"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9812999963760376,"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/probabilistic-logic","display_name":"Probabilistic logic","score":0.7355822920799255},{"id":"https://openalex.org/keywords/maximum-a-posteriori-estimation","display_name":"Maximum a posteriori estimation","score":0.5991178154945374},{"id":"https://openalex.org/keywords/prior-probability","display_name":"Prior probability","score":0.5322496891021729},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.49067890644073486},{"id":"https://openalex.org/keywords/biomolecular-structure","display_name":"Biomolecular structure","score":0.48818689584732056},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48467352986335754},{"id":"https://openalex.org/keywords/expectation\u2013maximization-algorithm","display_name":"Expectation\u2013maximization algorithm","score":0.47905075550079346},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4651412069797516},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4335877299308777},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.376969575881958},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37348300218582153},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26787471771240234},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.22638186812400818},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.14490064978599548},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.14180529117584229},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11600443720817566}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.7355822920799255},{"id":"https://openalex.org/C9810830","wikidata":"https://www.wikidata.org/wiki/Q635384","display_name":"Maximum a posteriori estimation","level":3,"score":0.5991178154945374},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.5322496891021729},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.49067890644073486},{"id":"https://openalex.org/C38111792","wikidata":"https://www.wikidata.org/wiki/Q15712714","display_name":"Biomolecular structure","level":3,"score":0.48818689584732056},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48467352986335754},{"id":"https://openalex.org/C182081679","wikidata":"https://www.wikidata.org/wiki/Q1275153","display_name":"Expectation\u2013maximization algorithm","level":3,"score":0.47905075550079346},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4651412069797516},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4335877299308777},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.376969575881958},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37348300218582153},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26787471771240234},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.22638186812400818},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.14490064978599548},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.14180529117584229},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11600443720817566},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/cibcb.2019.8791469","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2019.8791469","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"},{"id":"pmid:34661202","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34661202","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":"Proceedings of the ... IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology : CIBCB. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8515897","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8515897","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Symp Comput Intell Bioinforma Comput Biol","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/6a8fd548-b917-45fb-a285-f5466294dddf","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/6a8fd548-b917-45fb-a285-f5466294dddf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Moreta , L S , Al-Sibahi , A S , Theobald , D , Bullock , W , Rommes , B N , Manoukian , A & Hamelryck , T 2019 , A Probabilistic Programming Approach to Protein Structure Superposition . in G Baruzzo , S Daberdaku , B Di Camillo , S Furini , E D Giordano & G Nicosia (eds) , 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2019 . , 8791469 , IEEE , 16th IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2019 , Certosa di Pontignano, Siena , Italy , 09/07/2019 . https://doi.org/10.1109/CIBCB.2019.8791469","raw_type":"contributionToPeriodical"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8515897","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8515897","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc IEEE Symp Comput Intell Bioinforma Comput Biol","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1482971402","https://openalex.org/W1552850027","https://openalex.org/W1810943226","https://openalex.org/W1993267444","https://openalex.org/W2092464013","https://openalex.org/W2103956655","https://openalex.org/W2108107014","https://openalex.org/W2114850508","https://openalex.org/W2128175348","https://openalex.org/W2130479394","https://openalex.org/W2135303325","https://openalex.org/W2146502635","https://openalex.org/W2217402295","https://openalex.org/W2897613819","https://openalex.org/W2899771611","https://openalex.org/W2952317511","https://openalex.org/W2964321317","https://openalex.org/W6681435938","https://openalex.org/W6755447188","https://openalex.org/W6756040250"],"related_works":["https://openalex.org/W1839961359","https://openalex.org/W2075146114","https://openalex.org/W1783992599","https://openalex.org/W2114899076","https://openalex.org/W2100805585","https://openalex.org/W2045588782","https://openalex.org/W2124697778","https://openalex.org/W2135468550","https://openalex.org/W2133422797","https://openalex.org/W1571591724"],"abstract_inverted_index":{"Optimal":[0],"superposition":[1,50],"of":[2,24,48,57,80,142,154],"protein":[3,29,49,167],"structures":[4,30],"or":[5,163],"other":[6],"biological":[7],"molecules":[8],"is":[9,39,134],"crucial":[10],"for":[11,139],"understanding":[12],"their":[13],"structure,":[14],"function,":[15],"dynamics":[16],"and":[17,55,91,124],"evolution.":[18],"Here,":[19],"we":[20,150],"investigate":[21],"the":[22,42,68,78,81,140,152,155],"use":[23,153],"probabilistic":[25,46,69,132,144,172],"programming":[26,70,133],"to":[27],"superimpose":[28],"guided":[31],"by":[32],"a":[33,45,135,159],"Bayesian":[34,143,166],"model.":[35],"Our":[36],"model":[37,47,64,157,162],"THESEUS-PP":[38,110,156],"based":[40,51],"on":[41,52],"THESEUS":[43,84,100],"model,":[44],"rotation,":[53,121],"translation":[54],"perturbation":[56],"an":[58],"underlying,":[59],"latent":[60,125],"mean":[61,126],"structure.":[62,127,148],"The":[63,128],"was":[65],"implemented":[66],"in":[67,165],"language":[71],"Pyro.":[72],"Unlike":[73],"conventional":[74],"methods":[75],"that":[76,131],"minimize":[77],"sum":[79],"squared":[82],"distances,":[83],"takes":[85],"into":[86],"account":[87],"correlated":[88],"atom":[89,94],"positions":[90,95],"heteroscedasticity":[92],"(ie.":[93],"can":[96],"feature":[97],"different":[98],"variances).":[99],"performs":[101],"maximum":[102,113],"likelihood":[103,164],"estimation":[104,116],"using":[105,117,170],"iterative":[106],"expectation-maximization.":[107],"In":[108],"contrast,":[109],"allows":[111],"automated":[112],"a-posteriori":[114],"(MAP)":[115],"suitable":[118,160],"priors":[119],"over":[120],"translation,":[122],"variances":[123],"results":[129],"indicate":[130],"powerful":[136],"new":[137],"paradigm":[138],"formulation":[141],"models":[145],"concerning":[146],"biomolecular":[147],"Specifically,":[149],"envision":[151],"as":[158],"error":[161],"structure":[168],"prediction":[169],"deep":[171],"programming.":[173]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}