{"id":"https://openalex.org/W2048154580","doi":"https://doi.org/10.1371/journal.pcbi.1003847","title":"Improving Contact Prediction along Three Dimensions","display_name":"Improving Contact Prediction along Three Dimensions","publication_year":2014,"publication_date":"2014-10-09","ids":{"openalex":"https://openalex.org/W2048154580","doi":"https://doi.org/10.1371/journal.pcbi.1003847","mag":"2048154580","pmid":"https://pubmed.ncbi.nlm.nih.gov/25299132"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003847","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003847","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003847&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":["arxiv","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.1003847&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026008808","display_name":"Christoph Feinauer","orcid":"https://orcid.org/0000-0002-8941-7333"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Christoph Feinauer","raw_affiliation_strings":["DISAT and Center for Computational Sciences, Politecnico Torino, Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DISAT and Center for Computational Sciences, Politecnico Torino, Torino, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057759361","display_name":"Marcin J. Skwark","orcid":"https://orcid.org/0000-0002-2022-6766"},"institutions":[{"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":"Marcin J. Skwark","raw_affiliation_strings":["Department of Information and Computer Science, Aalto University, Aalto, Finland; Aalto Science Institute (AScI), Aalto University, Aalto, Finland","Aalto Science Institute (AScI), Aalto University, Aalto, Finland","Department of Information and Computer Science, Aalto University, Aalto, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computer Science, Aalto University, Aalto, Finland; Aalto Science Institute (AScI), Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Aalto Science Institute (AScI), Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Department of Information and Computer Science, Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011435835","display_name":"Andrea Pagnani","orcid":"https://orcid.org/0000-0002-6509-0807"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]},{"id":"https://openalex.org/I4210123319","display_name":"Italian institute for Genomic Medicine","ror":"https://ror.org/036054d36","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210123319"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Pagnani","raw_affiliation_strings":["DISAT and Center for Computational Sciences, Politecnico Torino, Torino, Italy; Human Genetics Foundation-Torino, Molecular Biotechnology Center, Torino, Italy","DISAT and Center for Computational Sciences, Politecnico Torino, Torino, Italy","Human Genetics Foundation-Torino, Molecular Biotechnology Center, Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DISAT and Center for Computational Sciences, Politecnico Torino, Torino, Italy; Human Genetics Foundation-Torino, Molecular Biotechnology Center, Torino, Italy","institution_ids":["https://openalex.org/I177477856","https://openalex.org/I4210123319"]},{"raw_affiliation_string":"DISAT and Center for Computational Sciences, Politecnico Torino, Torino, Italy","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"Human Genetics Foundation-Torino, Molecular Biotechnology Center, Torino, Italy","institution_ids":["https://openalex.org/I4210123319"]}]},{"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/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]},{"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":true,"raw_author_name":"Erik Aurell","raw_affiliation_strings":["Department of Information and Computer Science, Aalto University, Aalto, Finland; Aalto Science Institute (AScI), Aalto University, Aalto, Finland; Department of Computational Biology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden","Aalto Science Institute (AScI), Aalto University, Aalto, Finland","Department of Computational Biology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden","Department of Information and Computer Science, Aalto University, Aalto, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computer Science, Aalto University, Aalto, Finland; Aalto Science Institute (AScI), Aalto University, Aalto, Finland; Department of Computational Biology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Aalto Science Institute (AScI), Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Department of Computational Biology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden","institution_ids":["https://openalex.org/I4210135511","https://openalex.org/I86987016"]},{"raw_affiliation_string":"Department of Information and Computer Science, Aalto University, Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5047019776"],"corresponding_institution_ids":["https://openalex.org/I4210135511","https://openalex.org/I86987016","https://openalex.org/I9927081"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.2375,"has_fulltext":true,"cited_by_count":96,"citation_normalized_percentile":{"value":0.97462787,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"10","issue":"10","first_page":"e1003847","last_page":"e1003847"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10591","display_name":"Theoretical and Computational Physics","score":0.9833999872207642,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9829000234603882,"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/sequence","display_name":"Sequence (biology)","score":0.6380687355995178},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5775502920150757},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5750656127929688},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.5343522429466248},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.529360830783844},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5111742615699768},{"id":"https://openalex.org/keywords/dimension","display_name":"Dimension (graph theory)","score":0.5085431337356567},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.46591734886169434},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45703282952308655},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4530595541000366},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4301525056362152},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4242347180843353},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4233311414718628},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3610544800758362},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23644718527793884},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21052926778793335},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1510295271873474},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13347265124320984},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11060541868209839},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1080399751663208}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6380687355995178},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5775502920150757},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5750656127929688},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.5343522429466248},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.529360830783844},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5111742615699768},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.5085431337356567},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.46591734886169434},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45703282952308655},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4530595541000366},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4301525056362152},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4242347180843353},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4233311414718628},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3610544800758362},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23644718527793884},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21052926778793335},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1510295271873474},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13347265124320984},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11060541868209839},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1080399751663208},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":11,"locations":[{"id":"doi:10.1371/journal.pcbi.1003847","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003847","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003847&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:25299132","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25299132","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:arXiv.org:1403.0379","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1403.0379","pdf_url":"https://arxiv.org/pdf/1403.0379","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"},{"id":"pmh:oai:porto.polito.it:2568336","is_oa":true,"landing_page_url":"http://porto.polito.it/2568336/1/journal.pcbi.1003847_1_.pdf","pdf_url":"http://porto.polito.it/2568336/1/journal.pcbi.1003847_1_.pdf","source":{"id":"https://openalex.org/S4306402038","display_name":"PORTO Publications Open Repository TOrino (Politecnico di Torino)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177477856","host_organization_name":"Politecnico di Torino","host_organization_lineage":["https://openalex.org/I177477856"],"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":"ISSN:1553-734X","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4191875","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4191875","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.758.631","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.758.631","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/1403.0379.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.794.2253","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.794.2253","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/49/b9/pcbi.1003847.PMC4191875.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003847","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003847","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:aaltodoc.aalto.fi:123456789/28257","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/9fffb0bf-f287-41d3-93bb-47d2383dcdff","pdf_url":null,"source":{"id":"https://openalex.org/S4306401662","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:218963cc1828459ea88ef83f9aaee8f5","is_oa":true,"landing_page_url":"https://doaj.org/article/218963cc1828459ea88ef83f9aaee8f5","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 10, Iss 10, p e1003847 (2014)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1199463","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Improving_Contact_Prediction_along_Three_Dimensions_/1199463","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003847","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003847","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003847&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":[],"awards":[{"id":"https://openalex.org/G3207356259","display_name":null,"funder_award_id":"2007\u20132013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G393177772","display_name":null,"funder_award_id":"FP7 2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4781614665","display_name":"Statistical Physics Approaches to Networks Across Disciplines","funder_award_id":"290038","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5702163051","display_name":null,"funder_award_id":"FP7/2007","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6901317335","display_name":null,"funder_award_id":"290038","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2048154580.pdf","grobid_xml":"https://content.openalex.org/works/W2048154580.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W28766783","https://openalex.org/W1514077080","https://openalex.org/W1576267150","https://openalex.org/W1853158677","https://openalex.org/W1965511886","https://openalex.org/W1965839094","https://openalex.org/W1966816931","https://openalex.org/W1976666280","https://openalex.org/W1979762151","https://openalex.org/W1982583124","https://openalex.org/W2008545402","https://openalex.org/W2009570821","https://openalex.org/W2013425283","https://openalex.org/W2014706477","https://openalex.org/W2021769301","https://openalex.org/W2033806446","https://openalex.org/W2039092135","https://openalex.org/W2045777307","https://openalex.org/W2048310584","https://openalex.org/W2051210555","https://openalex.org/W2051545676","https://openalex.org/W2061042699","https://openalex.org/W2065921821","https://openalex.org/W2085277871","https://openalex.org/W2092006899","https://openalex.org/W2096915408","https://openalex.org/W2097230740","https://openalex.org/W2107517961","https://openalex.org/W2107676974","https://openalex.org/W2108067237","https://openalex.org/W2113358325","https://openalex.org/W2120340025","https://openalex.org/W2127138006","https://openalex.org/W2135621733","https://openalex.org/W2137566700","https://openalex.org/W2138551420","https://openalex.org/W2141885858","https://openalex.org/W2142331410","https://openalex.org/W2154115141","https://openalex.org/W2154643316","https://openalex.org/W2166701319","https://openalex.org/W2169478909","https://openalex.org/W2171641243","https://openalex.org/W2605068739","https://openalex.org/W3101056534","https://openalex.org/W4212920271","https://openalex.org/W4245668478","https://openalex.org/W4253932762","https://openalex.org/W4293052541","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W3037187668","https://openalex.org/W4234772502","https://openalex.org/W2380685755","https://openalex.org/W2252100032","https://openalex.org/W2963436428","https://openalex.org/W4400978025","https://openalex.org/W2918743509","https://openalex.org/W2734796617","https://openalex.org/W3083218341","https://openalex.org/W3034087822"],"abstract_inverted_index":{"Correlation":[0],"patterns":[1],"in":[2,31,76],"multiple":[3,140],"sequence":[4,51,66,141],"alignments":[5,142],"of":[6,19,40,78,131,147,171],"homologous":[7],"proteins":[8,172],"can":[9],"be":[10,155],"exploited":[11],"to":[12,25,35,44,63,108,189],"infer":[13,69],"information":[14],"on":[15],"the":[16,37,49,54,70,112,118,129,132,176,180],"three-dimensional":[17],"structure":[18],"their":[20],"members.":[21],"The":[22],"typical":[23],"pipeline":[24],"address":[26],"this":[27,32],"task,":[28],"which":[29,125],"we":[30,102,173],"paper":[33],"refer":[34],"as":[36,82,150,184,186],"three":[38,92,181],"dimensions":[39,93,182],"contact":[41,85],"prediction,":[42],"is":[43,106],"(i)":[45],"filter":[46],"and":[47,73],"align":[48],"raw":[50],"data":[52,152],"representing":[53],"evolutionarily":[55],"related":[56],"proteins;":[57],"(ii)":[58],"choose":[59],"a":[60,65,151,163,167],"predictive":[61],"model":[62,71],"describe":[64],"alignment;":[67],"(iii)":[68],"parameters":[72],"interpret":[74],"them":[75],"terms":[77],"structural":[79],"properties,":[80],"such":[81],"an":[83],"accurate":[84],"map.":[86],"We":[87],"show":[88,103,174],"here":[89],"that":[90,104,175],"all":[91],"are":[94,137,183],"important":[95],"for":[96,158],"overall":[97],"prediction":[98],"success.":[99],"In":[100],"particular,":[101],"it":[105],"possible":[107],"improve":[109],"significantly":[110],"along":[111,179],"second":[113],"dimension":[114],"by":[115,139],"going":[116],"beyond":[117],"pair-wise":[119],"Potts":[120,164],"models":[121],"from":[122,162],"statistical":[123],"physics,":[124],"have":[126],"hitherto":[127],"been":[128],"focus":[130],"field.":[133],"These":[134],"(simple)":[135],"extensions":[136],"motivated":[138],"often":[143],"containing":[144],"long":[145],"stretches":[146],"gaps":[148],"which,":[149],"feature,":[153],"would":[154],"rather":[156],"untypical":[157],"independent":[159],"samples":[160],"drawn":[161],"model.":[165],"Using":[166],"large":[168,185],"test":[169],"set":[170],"combined":[177],"improvements":[178],"any":[187],"reported":[188],"date.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":21},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
