{"id":"https://openalex.org/W2024005354","doi":"https://doi.org/10.1371/journal.pcbi.1003341","title":"Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison","display_name":"Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison","publication_year":2013,"publication_date":"2013-11-14","ids":{"openalex":"https://openalex.org/W2024005354","doi":"https://doi.org/10.1371/journal.pcbi.1003341","mag":"2024005354","pmid":"https://pubmed.ncbi.nlm.nih.gov/24244144"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003341","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003341","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003341&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":["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.1003341&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007997462","display_name":"Janez Konc","orcid":"https://orcid.org/0000-0003-0160-3375"},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Janez Konc","raw_affiliation_strings":["National Institute of Chemistry, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054295874","display_name":"Milan Hodo\u0161\u010dek","orcid":"https://orcid.org/0000-0002-6728-9318"},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Milan Hodo\u0161\u010dek","raw_affiliation_strings":["National Institute of Chemistry, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041911922","display_name":"Mitja Ogrizek","orcid":null},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Mitja Ogrizek","raw_affiliation_strings":["National Institute of Chemistry, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028394991","display_name":"Joanna Trykowska Konc","orcid":null},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Joanna Trykowska Konc","raw_affiliation_strings":["National Institute of Chemistry, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074495088","display_name":"Du\u0161anka Jane\u017ei\u010d","orcid":"https://orcid.org/0000-0003-4067-0116"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Du\u0161anka Jane\u017ei\u010d","raw_affiliation_strings":["National Institute of Chemistry, Ljubljana, Slovenia","University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]},{"raw_affiliation_string":"University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074495088"],"corresponding_institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.5116,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.81646779,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"11","first_page":"e1003341","last_page":"e1003341"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9994999766349792,"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/structural-genomics","display_name":"Structural genomics","score":0.6657748222351074},{"id":"https://openalex.org/keywords/endonuclease","display_name":"Endonuclease","score":0.5906514525413513},{"id":"https://openalex.org/keywords/thermotoga-maritima","display_name":"Thermotoga maritima","score":0.5882427096366882},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.554207980632782},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5483128428459167},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5404452085494995},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5280488133430481},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.509732186794281},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.49245724081993103},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.39324551820755005},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3182854652404785},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3104134202003479},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17472553253173828},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07876220345497131},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.06280618906021118}],"concepts":[{"id":"https://openalex.org/C192772702","wikidata":"https://www.wikidata.org/wiki/Q2583975","display_name":"Structural genomics","level":3,"score":0.6657748222351074},{"id":"https://openalex.org/C2777028655","wikidata":"https://www.wikidata.org/wiki/Q415601","display_name":"Endonuclease","level":3,"score":0.5906514525413513},{"id":"https://openalex.org/C2777002520","wikidata":"https://www.wikidata.org/wiki/Q7783261","display_name":"Thermotoga maritima","level":4,"score":0.5882427096366882},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.554207980632782},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5483128428459167},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5404452085494995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5280488133430481},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.509732186794281},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.49245724081993103},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.39324551820755005},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3182854652404785},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3104134202003479},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17472553253173828},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07876220345497131},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.06280618906021118},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"D020124","descriptor_name":"Thermotoga maritima","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020124","descriptor_name":"Thermotoga maritima","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020124","descriptor_name":"Thermotoga maritima","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1003341","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003341","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003341&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:24244144","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24244144","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:europepmc.org:2815883","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3828134","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.774.361","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.774.361","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/b8/db/pcbi.1003341.PMC3828134.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:59ea81141542427d8c9338edfa15acda","is_oa":true,"landing_page_url":"https://doaj.org/article/59ea81141542427d8c9338edfa15acda","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 9, Iss 11, p e1003341 (2013)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/850602","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Structure_Based_Function_Prediction_of_Uncharacterized_Protein_Using_Binding_Sites_Comparison_/850602","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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.1003341","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003341","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003341&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":[{"display_name":"Life below water","score":0.6800000071525574,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G6070106675","display_name":"Multiscale modeling and simulation of soft and biological matter in and out of equilibrium","funder_award_id":"P1-0002","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2024005354.pdf","grobid_xml":"https://content.openalex.org/works/W2024005354.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1505216348","https://openalex.org/W1965186869","https://openalex.org/W1975580333","https://openalex.org/W1978330227","https://openalex.org/W1983970695","https://openalex.org/W1984015691","https://openalex.org/W1986154009","https://openalex.org/W1996680929","https://openalex.org/W1997401305","https://openalex.org/W2001913949","https://openalex.org/W2008512283","https://openalex.org/W2015147525","https://openalex.org/W2018919352","https://openalex.org/W2019701333","https://openalex.org/W2028861967","https://openalex.org/W2029582401","https://openalex.org/W2034678374","https://openalex.org/W2035494017","https://openalex.org/W2035503835","https://openalex.org/W2042908061","https://openalex.org/W2051419785","https://openalex.org/W2055043387","https://openalex.org/W2061285367","https://openalex.org/W2062475405","https://openalex.org/W2065705570","https://openalex.org/W2068313448","https://openalex.org/W2068823829","https://openalex.org/W2085277871","https://openalex.org/W2093151204","https://openalex.org/W2096863497","https://openalex.org/W2097401561","https://openalex.org/W2097642323","https://openalex.org/W2130479394","https://openalex.org/W2132262459","https://openalex.org/W2138770756","https://openalex.org/W2141149420","https://openalex.org/W2141885858","https://openalex.org/W2146940292","https://openalex.org/W2149475400","https://openalex.org/W2151889113","https://openalex.org/W2160336334","https://openalex.org/W2162220273","https://openalex.org/W2169434145","https://openalex.org/W2183091601","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W2086222315","https://openalex.org/W1975509419","https://openalex.org/W2978951900","https://openalex.org/W2346580382","https://openalex.org/W2122730191","https://openalex.org/W2015390241","https://openalex.org/W2118652015","https://openalex.org/W2166261803","https://openalex.org/W1972763041","https://openalex.org/W2059333155"],"abstract_inverted_index":{"A":[0],"challenge":[1],"in":[2,36,49,146,162,182],"structural":[3,31],"genomics":[4],"is":[5,33,170,193],"prediction":[6],"of":[7,10,21,25,62,65,85,102,109,202,214,216],"the":[8,52,60,68,117,136,152],"function":[9,26,61,215],"uncharacterized":[11,217],"proteins.":[12,218],"When":[13],"proteins":[14,20],"cannot":[15],"be":[16,41,144,197,208],"related":[17],"to":[18,43,80,140,143,199,210],"other":[19],"known":[22,142],"activity,":[23,67],"identification":[24],"based":[27],"on":[28],"sequence":[29],"or":[30],"homology":[32],"impossible":[34],"and":[35,125,151,195],"such":[37],"cases":[38],"it":[39],"would":[40],"useful":[42,209],"assess":[44],"structurally":[45],"conserved":[46],"binding":[47,78,95,121,154,173],"sites":[48,96],"connection":[50],"with":[51,93,113,175],"protein's":[53],"function.":[54,204],"In":[55],"this":[56,110,127],"paper,":[57],"we":[58],"propose":[59,167],"a":[63,81,99,107,114,171],"protein":[64,70,112,201],"unknown":[66,203],"Tm1631":[69,111,169],"from":[71,116,158],"Thermotoga":[72],"maritima,":[73],"by":[74,129,135],"comparing":[75],"its":[76],"predicted":[77,134],"site":[79,101,122],"library":[82],"containing":[83],"thousands":[84],"candidate":[86],"structures.":[87],"The":[88,132],"comparison":[89],"revealed":[90],"numerous":[91],"similarities":[92],"nucleotide":[94],"including":[97],"specifically,":[98],"DNA-binding":[100],"endonuclease":[103,147,176],"IV.":[104],"We":[105,165],"constructed":[106],"model":[108,128,138,150],"DNA-ligand":[115],"newly":[118],"found":[119],"similar":[120],"using":[123],"ProBiS,":[124],"validated":[126],"molecular":[130],"dynamics.":[131],"interactions":[133],"Tm1631-DNA":[137],"corresponded":[139],"those":[141],"important":[145],"IV-DNA":[148],"complex":[149],"corresponding":[153],"free":[155],"energies,":[156],"calculated":[157],"these":[159],"models":[160],"were":[161],"close":[163],"agreement.":[164],"thus":[166],"that":[168,178],"DNA":[172,180],"enzyme":[174],"activity":[177],"recognizes":[179],"lesions":[181],"which":[183],"at":[184],"least":[185],"two":[186],"consecutive":[187],"nucleotides":[188],"are":[189],"unpaired.":[190],"Our":[191],"approach":[192],"general,":[194],"can":[196],"applied":[198],"any":[200],"It":[205],"might":[206],"also":[207],"guide":[211],"experimental":[212],"determination":[213]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}