{"id":"https://openalex.org/W2110586207","doi":"https://doi.org/10.1093/nar/gkn308","title":"3D-Fun: predicting enzyme function from structure","display_name":"3D-Fun: predicting enzyme function from structure","publication_year":2008,"publication_date":"2008-05-19","ids":{"openalex":"https://openalex.org/W2110586207","doi":"https://doi.org/10.1093/nar/gkn308","mag":"2110586207","pmid":"https://pubmed.ncbi.nlm.nih.gov/18515349"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn308","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn308","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkn308","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008863270","display_name":"Marcin von Grotthuss","orcid":"https://orcid.org/0000-0002-2850-1152"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]},{"id":"https://openalex.org/I4210132495","display_name":"BioInfoBank Institute","ror":"https://ror.org/0432q4w56","country_code":"PL","type":"nonprofit","lineage":["https://openalex.org/I4210132495"]}],"countries":["NL","PL"],"is_corresponding":false,"raw_author_name":"M. von Grotthuss","raw_affiliation_strings":["CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands","CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802934949"]},{"raw_affiliation_string":"CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802934949","https://openalex.org/I4210132495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021916927","display_name":"Dariusz Plewczy\u0144ski","orcid":"https://orcid.org/0000-0002-3840-7610"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]},{"id":"https://openalex.org/I4210132495","display_name":"BioInfoBank Institute","ror":"https://ror.org/0432q4w56","country_code":"PL","type":"nonprofit","lineage":["https://openalex.org/I4210132495"]}],"countries":["NL","PL"],"is_corresponding":false,"raw_author_name":"D. Plewczynski","raw_affiliation_strings":["CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802934949","https://openalex.org/I4210132495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075419050","display_name":"Gert Vriend","orcid":"https://orcid.org/0000-0002-1067-7053"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]},{"id":"https://openalex.org/I4210132495","display_name":"BioInfoBank Institute","ror":"https://ror.org/0432q4w56","country_code":"PL","type":"nonprofit","lineage":["https://openalex.org/I4210132495"]}],"countries":["NL","PL"],"is_corresponding":false,"raw_author_name":"G. Vriend","raw_affiliation_strings":["CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802934949","https://openalex.org/I4210132495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036708265","display_name":"Leszek Rychlewski","orcid":null},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]},{"id":"https://openalex.org/I4210132495","display_name":"BioInfoBank Institute","ror":"https://ror.org/0432q4w56","country_code":"PL","type":"nonprofit","lineage":["https://openalex.org/I4210132495"]}],"countries":["NL","PL"],"is_corresponding":false,"raw_author_name":"L. Rychlewski","raw_affiliation_strings":["CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands and 2 BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I2802934949","https://openalex.org/I4210132495"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.6505,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.68542529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"36","issue":"Web Server","first_page":"W303","last_page":"W307"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10887","display_name":"Bioinformatics and Genomic Networks","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/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/T10044","display_name":"Protein Structure and Dynamics","score":0.9954000115394592,"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/software","display_name":"Software","score":0.7255002856254578},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.7154862880706787},{"id":"https://openalex.org/keywords/structural-genomics","display_name":"Structural genomics","score":0.6989149451255798},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6425327658653259},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.606957197189331},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.5105584859848022},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.48237624764442444},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.43659085035324097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42979300022125244},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4296576976776123},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.4286458492279053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4274802803993225},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.423308789730072},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3504118323326111},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3139922022819519},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.3055726885795593},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2102464735507965},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.1791696846485138},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17794111371040344},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1731458604335785},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.15752625465393066},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.138764888048172},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09863656759262085}],"concepts":[{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.7255002856254578},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.7154862880706787},{"id":"https://openalex.org/C192772702","wikidata":"https://www.wikidata.org/wiki/Q2583975","display_name":"Structural genomics","level":3,"score":0.6989149451255798},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6425327658653259},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.606957197189331},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.5105584859848022},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.48237624764442444},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.43659085035324097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42979300022125244},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4296576976776123},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.4286458492279053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4274802803993225},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.423308789730072},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3504118323326111},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3139922022819519},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.3055726885795593},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2102464735507965},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.1791696846485138},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17794111371040344},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1731458604335785},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.15752625465393066},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.138764888048172},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09863656759262085},{"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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkn308","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn308","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18515349","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18515349","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2447717","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447717","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:repository.ubn.ru.nl:2066/70748","is_oa":false,"landing_page_url":"http://hdl.handle.net/2066/70748","pdf_url":null,"source":{"id":"https://openalex.org/S4306401067","display_name":"Radboud Repository (Radboud University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145872427","host_organization_name":"Radboud University Nijmegen","host_organization_lineage":["https://openalex.org/I145872427"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 36, Web Server issue, pp. W303-7","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn308","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn308","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4099999964237213,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322733","display_name":"Ministerstwo Edukacji i Nauki","ror":"https://ror.org/05dwvd537"},{"id":"https://openalex.org/F4320328786","display_name":"Norwegian Biodiversity Information Centre","ror":"https://ror.org/04jnzhb65"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W42096393","https://openalex.org/W1955025754","https://openalex.org/W1971646616","https://openalex.org/W1971690451","https://openalex.org/W2016088798","https://openalex.org/W2043199972","https://openalex.org/W2107946060","https://openalex.org/W2108211735","https://openalex.org/W2141807666","https://openalex.org/W2141885858","https://openalex.org/W2142642738","https://openalex.org/W2151600636","https://openalex.org/W2152524078","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W2147095787","https://openalex.org/W2067364375","https://openalex.org/W2116930553","https://openalex.org/W1992931978","https://openalex.org/W1966852334","https://openalex.org/W959899326","https://openalex.org/W2122849532","https://openalex.org/W1600613454","https://openalex.org/W2100494857","https://openalex.org/W2110586207"],"abstract_inverted_index":{"The":[0,93,118,210],"'omics'":[1],"revolution":[2],"is":[3,45,55,97,109,168],"causing":[4],"a":[5,30,85,100],"flurry":[6],"of":[7,21,23,38,43,63,84],"data":[8],"that":[9,72,102],"all":[10,115,133],"needs":[11],"to":[12,17,80,174],"be":[13,27,74,207,213],"annotated":[14,28],"for":[15,112],"it":[16],"become":[18],"useful.":[19],"Sequences":[20],"proteins":[22,37,64,151],"unknown":[24,66,91],"function":[25,32,83,161,197],"can":[26,73,212],"with":[29,36,48,65,87,132,150,152,159,202],"putative":[31],"by":[33,137],"comparing":[34],"them":[35,131],"known":[39,88,134,153],"function.":[40,67,92],"This":[41,167],"form":[42],"annotation":[44],"typically":[46],"performed":[47],"BLAST":[49,176],"or":[50,217],"similar":[51,171],"software.":[52,144],"Structural":[53],"genomics":[54],"nowadays":[56],"also":[57],"bringing":[58],"us":[59],"three":[60],"dimensional":[61],"structures":[62,136],"We":[68],"present":[69],"here":[70],"software":[71],"used":[75],"when":[76],"sequence":[77],"comparisons":[78],"fail":[79],"determine":[81],"the":[82,125,142,181,191],"protein":[86,122,135],"structure":[89],"but":[90,198],"software,":[94],"called":[95],"3D-Fun,":[96],"implemented":[98],"as":[99],"server":[101,211],"runs":[103],"at":[104,114,215,218],"several":[105],"European":[106],"institutes":[107],"and":[108,129,162],"freely":[110],"available":[111,208],"everybody":[113],"these":[116,155],"sites.":[117],"3D-Fun":[119,192],"servers":[120],"accept":[121],"coordinates":[123],"in":[124,172,178],"standard":[126],"PDB":[127],"format":[128],"compare":[130],"3D":[138,173],"structural":[139,146],"superposition":[140,182],"using":[141,186],"3D-Hit":[143],"If":[145],"hits":[147],"are":[148,156,184],"found":[149],"function,":[154],"listed":[157],"together":[158],"their":[160],"some":[163],"vital":[164],"comparison":[165],"statistics.":[166],"conceptually":[169],"very":[170],"what":[175],"does":[177],"1D.":[179],"Additionally,":[180],"results":[183],"displayed":[185],"interactive":[187],"graphics":[188],"facilities.":[189],"Currently,":[190],"system":[193],"only":[194],"predicts":[195],"enzyme":[196],"an":[199],"expanded":[200],"version":[201],"Gene":[203],"Ontology":[204],"predictions":[205],"will":[206],"soon.":[209],"accessed":[214],"http://3dfun.bioinfo.pl/":[216],"http://3dfun.cmbi.ru.nl/.":[219]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
