{"id":"https://openalex.org/W4405355882","doi":"https://doi.org/10.1093/bioinformatics/btae740","title":"DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence","display_name":"DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence","publication_year":2024,"publication_date":"2024-12-13","ids":{"openalex":"https://openalex.org/W4405355882","doi":"https://doi.org/10.1093/bioinformatics/btae740","pmid":"https://pubmed.ncbi.nlm.nih.gov/39672676"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae740","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae740","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae740/61156925/btae740.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae740/61156925/btae740.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078742786","display_name":"Jesse Durham","orcid":null},"institutions":[{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jesse Durham","raw_affiliation_strings":["Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407","https://openalex.org/I4210096815"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0003-4190-3065"},"institutions":[{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407","https://openalex.org/I4210096815"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025471816","display_name":"R. Dustin Schaeffer","orcid":"https://orcid.org/0000-0001-6502-1425"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard D Schaeffer","raw_affiliation_strings":["Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039591575","display_name":"Qian Cong","orcid":"https://orcid.org/0000-0002-8909-0414"},"institutions":[{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qian Cong","raw_affiliation_strings":["Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390,","Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center , Dallas, TX 75390,","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407","https://openalex.org/I4210096815"]},{"raw_affiliation_string":"Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States","institution_ids":["https://openalex.org/I867280407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5078742786"],"corresponding_institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I867280407"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4579,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.66173573,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"41","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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":0.9958999752998352,"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":0.9919999837875366,"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/parsing","display_name":"Parsing","score":0.6109309792518616},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.5367651581764221},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5356134176254272},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48453015089035034},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44225892424583435},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.4361313581466675},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4328952729701996},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4039071202278137},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.34799811244010925},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21684911847114563},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14106693863868713},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12030965089797974}],"concepts":[{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6109309792518616},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.5367651581764221},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5356134176254272},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48453015089035034},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44225892424583435},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.4361313581466675},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4328952729701996},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4039071202278137},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.34799811244010925},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21684911847114563},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14106693863868713},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12030965089797974},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","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":"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btae740","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae740","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae740/61156925/btae740.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39672676","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39672676","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt0qt2053h","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/0qt2053h","pdf_url":"https://escholarship.org/content/qt0qt2053h/qt0qt2053h.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 41, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11723527","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11723527","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11723527/pdf/btae740.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:ark:/13030/qt0qt2053h","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae740","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae740","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae740/61156925/btae740.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3529166876","display_name":null,"funder_award_id":"R01GM147367","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4033401657","display_name":null,"funder_award_id":"1K99AI180984-01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5903061775","display_name":null,"funder_award_id":"NIAID","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6563068377","display_name":null,"funder_award_id":"GM147367","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8331785794","display_name":null,"funder_award_id":"K99AI","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8988264984","display_name":null,"funder_award_id":"GM147367","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306196","display_name":"Welch Foundation","ror":"https://ror.org/00np6vq88"},{"id":"https://openalex.org/F4320319026","display_name":"Southwestern Medical Foundation","ror":"https://ror.org/038v75980"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405355882.pdf","grobid_xml":"https://content.openalex.org/works/W4405355882.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1585827898","https://openalex.org/W1965827393","https://openalex.org/W1998931368","https://openalex.org/W2006964552","https://openalex.org/W2008708467","https://openalex.org/W2019345165","https://openalex.org/W2098223336","https://openalex.org/W2120804283","https://openalex.org/W2124871329","https://openalex.org/W2133062651","https://openalex.org/W2133070552","https://openalex.org/W2138116388","https://openalex.org/W2142678478","https://openalex.org/W2798240061","https://openalex.org/W2950954328","https://openalex.org/W2954851300","https://openalex.org/W2972411752","https://openalex.org/W3106745904","https://openalex.org/W3159719254","https://openalex.org/W3177828909","https://openalex.org/W3203459683","https://openalex.org/W3211795435","https://openalex.org/W4229910120","https://openalex.org/W4288039132","https://openalex.org/W4312032102","https://openalex.org/W4324132673","https://openalex.org/W4365517193","https://openalex.org/W4375858802","https://openalex.org/W4378591473","https://openalex.org/W4384931454","https://openalex.org/W4389947479","https://openalex.org/W4393342758"],"related_works":["https://openalex.org/W2087903152","https://openalex.org/W2157190239","https://openalex.org/W2946599741","https://openalex.org/W2050908913","https://openalex.org/W2593264178","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2154205489","https://openalex.org/W1984316389"],"abstract_inverted_index":{"Pfam":[0],"and":[1,14],"corresponding":[2],"DPAM-AI":[3],"domains":[4],"are":[5],"at":[6,12],"http://prodata.swmed.edu/DPAM-pfam/.":[7],"Our":[8],"code":[9],"is":[10],"deposited":[11],"https://github.com/Jsauce5p/DPAM/tree/dpam_ai,":[13],"updates":[15],"will":[16],"be":[17],"released":[18],"through":[19],"https://github.com/CongLabCode/DPAM.":[20]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
