{"id":"https://openalex.org/W2910754286","doi":"https://doi.org/10.1021/acs.jcim.8b00690","title":"DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings","display_name":"DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings","publication_year":2019,"publication_date":"2019-01-11","ids":{"openalex":"https://openalex.org/W2910754286","doi":"https://doi.org/10.1021/acs.jcim.8b00690","mag":"2910754286","pmid":"https://pubmed.ncbi.nlm.nih.gov/30632747"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00690","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00690","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023937063","display_name":"Aleksandra I. Jarmolinska","orcid":"https://orcid.org/0000-0002-1259-3611"},"institutions":[{"id":"https://openalex.org/I4210161028","display_name":"College of Europe, Warsaw","ror":"https://ror.org/055560x25","country_code":"PL","type":"education","lineage":["https://openalex.org/I172363630","https://openalex.org/I4210161028"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Aleksandra I. Jarmolinska","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland","College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0002-1259-3611","affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4210161028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034093132","display_name":"Qin Zhou","orcid":"https://orcid.org/0000-0002-7269-1731"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qin Zhou","raw_affiliation_strings":["Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States","institution_ids":["https://openalex.org/I162577319"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013867366","display_name":"Joanna I. Su\u0142kowska","orcid":"https://orcid.org/0000-0003-2452-0724"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Joanna I. Sulkowska","raw_affiliation_strings":["Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland","Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018611865","display_name":"Faruck Morcos","orcid":"https://orcid.org/0000-0001-6208-1561"},"institutions":[{"id":"https://openalex.org/I162577319","display_name":"The University of Texas at Dallas","ror":"https://ror.org/049emcs32","country_code":"US","type":"education","lineage":["https://openalex.org/I162577319"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Faruck Morcos","raw_affiliation_strings":["Center for Systems Biology, University of Texas at Dallas, Richardson, Texas 75080, United States","Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology, University of Texas at Dallas, Richardson, Texas 75080, United States","institution_ids":["https://openalex.org/I162577319"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States","institution_ids":["https://openalex.org/I162577319"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5013867366","https://openalex.org/A5018611865"],"corresponding_institution_ids":["https://openalex.org/I162577319","https://openalex.org/I4654613"],"apc_list":null,"apc_paid":null,"fwci":0.5154,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.63680237,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"59","issue":"2","first_page":"625","last_page":"629"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9979000091552734,"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":0.9968000054359436,"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/plug-in","display_name":"Plug-in","score":0.6914005279541016},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5786272287368774},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.47968053817749023},{"id":"https://openalex.org/keywords/monomer","display_name":"Monomer","score":0.465162068605423},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.4485984742641449},{"id":"https://openalex.org/keywords/statistical-analysis","display_name":"Statistical analysis","score":0.41835808753967285},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41392451524734497},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41333910822868347},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.41137710213661194},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3642248511314392},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32567447423934937},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.18925568461418152},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18384861946105957},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14455938339233398},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13787364959716797},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1097995936870575}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.6914005279541016},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5786272287368774},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.47968053817749023},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.465162068605423},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.4485984742641449},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.41835808753967285},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41392451524734497},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41333910822868347},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.41137710213661194},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3642248511314392},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32567447423934937},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.18925568461418152},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18384861946105957},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14455938339233398},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13787364959716797},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1097995936870575},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.8b00690","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00690","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:30632747","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30632747","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2853708676","display_name":null,"funder_award_id":"2012/07/E/NZ1/01900","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320307844","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1229175411","https://openalex.org/W1686007471","https://openalex.org/W1965839094","https://openalex.org/W1970483693","https://openalex.org/W1976666280","https://openalex.org/W1979762151","https://openalex.org/W1981264193","https://openalex.org/W2008545402","https://openalex.org/W2013425283","https://openalex.org/W2034557959","https://openalex.org/W2061042699","https://openalex.org/W2065921821","https://openalex.org/W2085036090","https://openalex.org/W2085211779","https://openalex.org/W2109839728","https://openalex.org/W2113358325","https://openalex.org/W2130479394","https://openalex.org/W2155075558","https://openalex.org/W2171641243","https://openalex.org/W2203425081","https://openalex.org/W2342766640","https://openalex.org/W2401397121","https://openalex.org/W2498485322","https://openalex.org/W2559132852","https://openalex.org/W2611175157","https://openalex.org/W2620385970","https://openalex.org/W2951188778","https://openalex.org/W3100820581"],"related_works":["https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W631546281","https://openalex.org/W4206501676","https://openalex.org/W88292646","https://openalex.org/W2266220644"],"abstract_inverted_index":{"Direct":[0],"coupling":[1],"analysis":[2],"(DCA)":[3],"is":[4,123],"a":[5,38],"statistical":[6],"modeling":[7],"framework":[8],"designed":[9],"to":[10,37,50,56,59,87],"uncover":[11],"relevant":[12],"molecular":[13,103],"evolutionary":[14,32],"relationships":[15],"from":[16,127],"biological":[17],"sequences.":[18],"Although":[19],"DCA":[20],"has":[21],"been":[22],"successfully":[23],"used":[24],"in":[25,85,99],"several":[26],"applications,":[27],"mapping":[28],"and":[29,34,46,62,70,83,105],"visualizing":[30],"of":[31,41,91,97],"couplings":[33],"direct":[35],"information":[36],"particular":[39],"set":[40],"molecules":[42],"requires":[43],"multiple":[44,112],"steps":[45],"could":[47],"be":[48,81,116],"prone":[49],"errors.":[51],"DCA-MOL":[52,122],"extends":[53],"PyMOL":[54],"functionality":[55],"allow":[57],"users":[58],"interactively":[60],"analyze":[61],"visualize":[63],"coevolutionary":[64],"residue-residue":[65,92],"interactions":[66,98],"between":[67],"contact":[68,93],"maps":[69],"structures.":[71],"True":[72],"positive":[73],"rates":[74],"for":[75,125],"the":[76,89],"top":[77],"N":[78],"pairs":[79],"can":[80,115],"computed":[82],"visualized":[84],"real-time":[86],"evaluate":[88],"quality":[90],"predictions.":[94],"Different":[95],"types":[96],"monomeric":[100],"proteins,":[101],"RNA,":[102],"interfaces,":[104],"protein":[106,113],"conformational":[107],"dynamics":[108],"as":[109,111],"well":[110],"complexes":[114],"studied":[117],"efficiently":[118],"within":[119],"one":[120],"application.":[121],"available":[124],"download":[126],"http://dca-mol.cent.uw.edu.pl.":[128]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
