{"id":"https://openalex.org/W2048310584","doi":"https://doi.org/10.1016/j.jcp.2014.07.024","title":"Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences","display_name":"Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences","publication_year":2014,"publication_date":"2014-07-25","ids":{"openalex":"https://openalex.org/W2048310584","doi":"https://doi.org/10.1016/j.jcp.2014.07.024","mag":"2048310584"},"language":"en","primary_location":{"id":"doi:10.1016/j.jcp.2014.07.024","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jcp.2014.07.024","pdf_url":null,"source":{"id":"https://openalex.org/S148709879","display_name":"Journal of Computational Physics","issn_l":"0021-9991","issn":["0021-9991","1090-2716"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Physics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1401.4832","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025716847","display_name":"Magnus Ekeberg","orcid":null},"institutions":[{"id":"https://openalex.org/I4210135511","display_name":"AlbaNova","ror":"https://ror.org/044kkfr75","country_code":"SE","type":"facility","lineage":["https://openalex.org/I4210135511"]},{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Magnus Ekeberg","raw_affiliation_strings":["Department of Computational Biology, AlbaNova University Centre, 106 91 Stockholm, Sweden","Engineering Physics Program, KTH Royal Institute of Technology, SE-100 77 Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, AlbaNova University Centre, 106 91 Stockholm, Sweden","institution_ids":["https://openalex.org/I4210135511"]},{"raw_affiliation_string":"Engineering Physics Program, KTH Royal Institute of Technology, SE-100 77 Stockholm, Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005255184","display_name":"Tuomo Hartonen","orcid":"https://orcid.org/0000-0002-5535-1698"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tuomo Hartonen","raw_affiliation_strings":["Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland","The Master's Degree Programme in Translational Medicine, Biomedicum Helsinki, FI-00014 University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"The Master's Degree Programme in Translational Medicine, Biomedicum Helsinki, FI-00014 University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047019776","display_name":"Erik Aurell","orcid":"https://orcid.org/0000-0003-4906-3603"},"institutions":[{"id":"https://openalex.org/I4210135511","display_name":"AlbaNova","ror":"https://ror.org/044kkfr75","country_code":"SE","type":"facility","lineage":["https://openalex.org/I4210135511"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","SE"],"is_corresponding":false,"raw_author_name":"Erik Aurell","raw_affiliation_strings":["Aalto Science Institute, PO Box 15600, FI-00076 Aalto, Finland","Department of Computational Biology, AlbaNova University Centre, 106 91 Stockholm, Sweden","Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aalto Science Institute, PO Box 15600, FI-00076 Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Department of Computational Biology, AlbaNova University Centre, 106 91 Stockholm, Sweden","institution_ids":["https://openalex.org/I4210135511"]},{"raw_affiliation_string":"Department of Information and Computer Science, Aalto University, PO Box 15400, FI-00076 Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025716847"],"corresponding_institution_ids":["https://openalex.org/I4210135511","https://openalex.org/I86987016"],"apc_list":{"value":3750,"currency":"USD","value_usd":3750},"apc_paid":null,"fwci":5.4602,"has_fulltext":false,"cited_by_count":207,"citation_normalized_percentile":{"value":0.96831519,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"276","issue":null,"first_page":"341","last_page":"356"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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":0.9972000122070312,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9969000220298767,"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/parallelizable-manifold","display_name":"Parallelizable manifold","score":0.8649002313613892},{"id":"https://openalex.org/keywords/maximization","display_name":"Maximization","score":0.5778334140777588},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.543962836265564},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5290305614471436},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.5107407569885254},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.47195401787757874},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.45278072357177734},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3959012031555176},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3685857057571411},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3033769726753235},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2792816758155823},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20078131556510925},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.19239675998687744},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09437233209609985}],"concepts":[{"id":"https://openalex.org/C148047603","wikidata":"https://www.wikidata.org/wiki/Q1014612","display_name":"Parallelizable manifold","level":2,"score":0.8649002313613892},{"id":"https://openalex.org/C2776330181","wikidata":"https://www.wikidata.org/wiki/Q18358244","display_name":"Maximization","level":2,"score":0.5778334140777588},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.543962836265564},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5290305614471436},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.5107407569885254},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.47195401787757874},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.45278072357177734},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3959012031555176},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3685857057571411},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3033769726753235},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2792816758155823},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20078131556510925},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.19239675998687744},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09437233209609985},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1016/j.jcp.2014.07.024","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jcp.2014.07.024","pdf_url":null,"source":{"id":"https://openalex.org/S148709879","display_name":"Journal of Computational Physics","issn_l":"0021-9991","issn":["0021-9991","1090-2716"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Physics","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1401.4832","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1401.4832","pdf_url":"https://arxiv.org/pdf/1401.4832","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1401.4832","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1401.4832","pdf_url":"https://arxiv.org/pdf/1401.4832","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W28766783","https://openalex.org/W136234207","https://openalex.org/W1494453148","https://openalex.org/W1514077080","https://openalex.org/W1540530720","https://openalex.org/W1585607520","https://openalex.org/W1853158677","https://openalex.org/W1966816931","https://openalex.org/W1977436723","https://openalex.org/W1979762151","https://openalex.org/W1982583124","https://openalex.org/W1997338824","https://openalex.org/W2008545402","https://openalex.org/W2013382823","https://openalex.org/W2013425283","https://openalex.org/W2014706477","https://openalex.org/W2015208937","https://openalex.org/W2017285544","https://openalex.org/W2018292899","https://openalex.org/W2021769301","https://openalex.org/W2039092135","https://openalex.org/W2048154580","https://openalex.org/W2051545676","https://openalex.org/W2054570677","https://openalex.org/W2059151864","https://openalex.org/W2061042699","https://openalex.org/W2085277871","https://openalex.org/W2086923559","https://openalex.org/W2091307684","https://openalex.org/W2099946731","https://openalex.org/W2101218312","https://openalex.org/W2107517961","https://openalex.org/W2113358325","https://openalex.org/W2119135250","https://openalex.org/W2120340025","https://openalex.org/W2120836664","https://openalex.org/W2121444044","https://openalex.org/W2122011799","https://openalex.org/W2127138006","https://openalex.org/W2137566700","https://openalex.org/W2138771217","https://openalex.org/W2141885858","https://openalex.org/W2146891463","https://openalex.org/W2164684045","https://openalex.org/W2165739018","https://openalex.org/W2166701319","https://openalex.org/W2169478909","https://openalex.org/W2171641243","https://openalex.org/W2402457502","https://openalex.org/W2952120503","https://openalex.org/W3099405535","https://openalex.org/W3099792582","https://openalex.org/W3101056534","https://openalex.org/W3103325978","https://openalex.org/W3144984470","https://openalex.org/W4249030130","https://openalex.org/W4293052541","https://openalex.org/W4320301318","https://openalex.org/W4385643431","https://openalex.org/W6630732884","https://openalex.org/W6654704429","https://openalex.org/W6683816936","https://openalex.org/W6831485455"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W4287117424","https://openalex.org/W4387506531","https://openalex.org/W4238433571","https://openalex.org/W3174044702","https://openalex.org/W2967848559","https://openalex.org/W4299831724"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-10-10T00:00:00"}
