{"id":"https://openalex.org/W2135303325","doi":"https://doi.org/10.1093/bioinformatics/bts243","title":"Optimal simultaneous superpositioning of multiple structures with missing data","display_name":"Optimal simultaneous superpositioning of multiple structures with missing data","publication_year":2012,"publication_date":"2012-04-27","ids":{"openalex":"https://openalex.org/W2135303325","doi":"https://doi.org/10.1093/bioinformatics/bts243","mag":"2135303325"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/15/1972/48875339/bioinformatics_28_15_1972.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/15/1972/48875339/bioinformatics_28_15_1972.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":true,"raw_author_name":"Douglas L. Theobald","raw_affiliation_strings":["Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02454, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02454, USA","institution_ids":["https://openalex.org/I6902469"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016019597","display_name":"P.A. Steindel","orcid":null},"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":"Phillip A. Steindel","raw_affiliation_strings":["Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02454, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02454, USA","institution_ids":["https://openalex.org/I6902469"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5046700536"],"corresponding_institution_ids":["https://openalex.org/I6902469"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6136,"has_fulltext":true,"cited_by_count":96,"citation_normalized_percentile":{"value":0.83169706,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"28","issue":"15","first_page":"1972","last_page":"1979"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9294999837875366,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9294999837875366,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9169999957084656,"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":0.9028000235557556,"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/computer-science","display_name":"Computer science","score":0.7568161487579346},{"id":"https://openalex.org/keywords/superposition-principle","display_name":"Superposition principle","score":0.7462846040725708},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.642316997051239},{"id":"https://openalex.org/keywords/data-point","display_name":"Data point","score":0.5055685043334961},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4655483663082123},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.4173364043235779},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3727147579193115},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34905827045440674},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1694350242614746},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12000921368598938}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7568161487579346},{"id":"https://openalex.org/C27753989","wikidata":"https://www.wikidata.org/wiki/Q284885","display_name":"Superposition principle","level":2,"score":0.7462846040725708},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.642316997051239},{"id":"https://openalex.org/C21080849","wikidata":"https://www.wikidata.org/wiki/Q13611879","display_name":"Data point","level":2,"score":0.5055685043334961},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4655483663082123},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.4173364043235779},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3727147579193115},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34905827045440674},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1694350242614746},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12000921368598938},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/15/1972/48875339/bioinformatics_28_15_1972.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"mag:22543369","is_oa":false,"landing_page_url":"http://eprints.icrisat.ac.in/580/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.991.6207","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.991.6207","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/04/27/bioinformatics.bts243.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3400950","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3400950","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/15/1972/48875339/bioinformatics_28_15_1972.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3218872511","display_name":null,"funder_award_id":"GM094468","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4691191956","display_name":null,"funder_award_id":"GM096053","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135303325.pdf","grobid_xml":"https://content.openalex.org/works/W2135303325.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W33507944","https://openalex.org/W281649968","https://openalex.org/W1490229695","https://openalex.org/W1534782460","https://openalex.org/W1545085620","https://openalex.org/W1584531376","https://openalex.org/W1884696523","https://openalex.org/W1966679395","https://openalex.org/W1967538863","https://openalex.org/W1975216864","https://openalex.org/W1985810115","https://openalex.org/W1993402893","https://openalex.org/W1997782631","https://openalex.org/W2028034301","https://openalex.org/W2031901496","https://openalex.org/W2032618685","https://openalex.org/W2042516820","https://openalex.org/W2045366578","https://openalex.org/W2049633694","https://openalex.org/W2060999146","https://openalex.org/W2067129729","https://openalex.org/W2078537874","https://openalex.org/W2102162967","https://openalex.org/W2103956655","https://openalex.org/W2115451817","https://openalex.org/W2117853077","https://openalex.org/W2121293808","https://openalex.org/W2126016150","https://openalex.org/W2131301342","https://openalex.org/W2133956643","https://openalex.org/W2146932984","https://openalex.org/W2148823738","https://openalex.org/W2165969670","https://openalex.org/W2168964504","https://openalex.org/W2433700685","https://openalex.org/W2477521491","https://openalex.org/W2767905780","https://openalex.org/W3148198191","https://openalex.org/W3148930403","https://openalex.org/W3179903767","https://openalex.org/W4241492945","https://openalex.org/W4242817406","https://openalex.org/W4388322985","https://openalex.org/W6646936755","https://openalex.org/W7037644959","https://openalex.org/W7062067314","https://openalex.org/W7071437906"],"related_works":["https://openalex.org/W4308749380","https://openalex.org/W2037841693","https://openalex.org/W4380150146","https://openalex.org/W3024870410","https://openalex.org/W2410652950","https://openalex.org/W2372481764","https://openalex.org/W1977264433","https://openalex.org/W4283773154","https://openalex.org/W2746368218","https://openalex.org/W3139174110"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Superpositioning":[2],"is":[3,81],"an":[4,119],"essential":[5],"technique":[6,137],"in":[7,36,41,166],"structural":[8],"biology":[9],"that":[10,72],"facilitates":[11],"the":[12,33,37,54,77,93,98,104,125,131,149,191],"comparison":[13],"and":[14,88,148,158,179],"analysis":[15],"of":[16,32,70,106,124],"conformational":[17],"differences":[18],"among":[19,75],"topologically":[20],"similar":[21],"structures.":[22,39,78,174],"Performing":[23],"a":[24,27,68,107,114,134,154,169],"superposition":[25,59,108,121],"requires":[26],"one-to-one":[28],"correspondence,":[29],"or":[30],"alignment,":[31],"point":[34],"sets":[35],"different":[38],"However,":[40],"practice,":[42],"some":[43,123],"points":[44,71],"are":[45,73,127,164,187,204],"usually":[46],"\u2018missing\u2019":[47],"from":[48,196],"several":[49],"structures,":[50],"for":[51,117,138,171,183],"example,":[52],"when":[53,122],"alignment":[55],"contains":[56],"gaps.":[57],"Current":[58],"methods":[60,161],"deal":[61],"with":[62,140],"missing":[63,101],"data":[64,126,203],"simply":[65],"by":[66],"superpositioning":[67,172],"subset":[69],"shared":[74],"all":[76],"This":[79],"practice":[80],"inefficient,":[82],"as":[83,153],"it":[84,89],"ignores":[85],"important":[86],"data,":[87,142],"fails":[90],"to":[91,143],"satisfy":[92],"common":[94],"least-squares":[95,151],"criterion.":[96],"In":[97],"extreme,":[99],"disregarding":[100],"positions":[102],"prohibits":[103],"calculation":[105],"altogether.":[109],"Results:":[110],"Here,":[111],"we":[112],"present":[113],"general":[115],"solution":[116,152],"determining":[118],"optimal":[120,150],"missing.":[128],"We":[129],"use":[130],"expectation\u2013maximization":[132],"algorithm,":[133],"classic":[135],"statistical":[136],"dealing":[139],"incomplete":[141],"find":[144],"both":[145],"maximum-likelihood":[146],"solutions":[147],"special":[155],"case.":[156],"Availability":[157],"implementation:":[159],"The":[160],"presented":[162],"here":[163],"implemented":[165],"THESEUS":[167],"2.0,":[168],"program":[170],"macromolecular":[173],"ANSI":[175],"C":[176],"source":[177,194],"code":[178],"selected":[180],"compiled":[181],"binaries":[182],"various":[184],"computing":[185],"platforms":[186],"freely":[188],"available":[189,205],"under":[190],"GNU":[192],"open":[193],"license":[195],"http://www.theseus3d.org.":[197],"Contact:":[198],"dtheobald@brandeis.edu":[199],"Supplementary":[200,202],"information:":[201],"at":[206],"Bioinformatics":[207],"online.":[208]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
