{"id":"https://openalex.org/W4399694730","doi":"https://doi.org/10.1093/bioinformatics/btae370","title":"RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments","display_name":"RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399694730","doi":"https://doi.org/10.1093/bioinformatics/btae370","pmid":"https://pubmed.ncbi.nlm.nih.gov/38870521"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae370","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae370/58230304/btae370.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/btae370/58230304/btae370.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017772944","display_name":"Sebastian Bittrich","orcid":"https://orcid.org/0000-0003-3576-0387"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sebastian Bittrich","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007270631","display_name":"Joan Segura","orcid":"https://orcid.org/0000-0001-5593-735X"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joan Segura","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003460293","display_name":"Jos\u00e9 M. Duarte","orcid":"https://orcid.org/0000-0002-9544-5621"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose M Duarte","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068648875","display_name":"S.K. Burley","orcid":"https://orcid.org/0000-0002-2487-9713"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen K Burley","raw_affiliation_strings":["Cancer Institute of New Jersey, Rutgers, The State University of New Jersey , New Brunswick, NJ 08901, United States","Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, United States","Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, United States","Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, United States","Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Cancer Institute of New Jersey, Rutgers, The State University of New Jersey , New Brunswick, NJ 08901, United States","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, United States","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, United States","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, United States","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061045572","display_name":"Yana Rose","orcid":"https://orcid.org/0000-0003-1018-5718"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yana Rose","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I181653535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5017772944"],"corresponding_institution_ids":["https://openalex.org/I181653535"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":40.4382,"has_fulltext":true,"cited_by_count":177,"citation_normalized_percentile":{"value":0.99930384,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"40","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9955000281333923,"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":0.9955000281333923,"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":0.9925000071525574,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.991599977016449,"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/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.9509472846984863},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.8407254219055176},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6872570514678955},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.6457130908966064},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5846912860870361},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5246836543083191},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5169300436973572},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4837615489959717},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.46254631876945496},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4211656153202057},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.36625587940216064},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36448195576667786},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3625461459159851},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33397993445396423},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2570532262325287},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.19228622317314148},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19181495904922485},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.170355886220932},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11362329125404358}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.9509472846984863},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.8407254219055176},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6872570514678955},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.6457130908966064},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5846912860870361},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5246836543083191},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5169300436973572},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4837615489959717},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.46254631876945496},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4211656153202057},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.36625587940216064},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36448195576667786},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3625461459159851},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33397993445396423},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2570532262325287},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.19228622317314148},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19181495904922485},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.170355886220932},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11362329125404358},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"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},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae370","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae370/58230304/btae370.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:38870521","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38870521","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:pubmedcentral.nih.gov:11212067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11212067","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11212067/pdf/btae370.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae370","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae370","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae370/58230304/btae370.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/G1316358765","display_name":null,"funder_award_id":"DBI-2321666","funder_id":"https://openalex.org/F4320332167","funder_display_name":"Directorate for Biological Sciences"},{"id":"https://openalex.org/G135050187","display_name":"BBSRC-NSF/BIO: From atoms to molecules to cells - Multi-scale tools and infrastructure for visualization of annotated 3D structure data","funder_award_id":"2129634","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2300401122","display_name":null,"funder_award_id":"DBI-2321666","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2800486080","display_name":"PDB Management by The Research Collaboratory for Structural Bioinformatics","funder_award_id":"2321666","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2805884023","display_name":null,"funder_award_id":"DBI-2129634","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G292810974","display_name":null,"funder_award_id":"DE-SC0019749","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science 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/G3748312226","display_name":null,"funder_award_id":"GM133198","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4562230808","display_name":null,"funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5584247792","display_name":null,"funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6351694128","display_name":"CIBR: BBSRC-NSF/BIO: Next generation Protein Data Bank - FACT infrastructure with value added FAIR data supporting diverse research and education user communities.","funder_award_id":"2019297","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6545353473","display_name":null,"funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6928499274","display_name":null,"funder_award_id":"DE-SC0019749","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7340972926","display_name":null,"funder_award_id":"other","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7452673040","display_name":null,"funder_award_id":"DBI-2019297","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7718543685","display_name":null,"funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"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":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399694730.pdf"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W2102245393","https://openalex.org/W2114854952","https://openalex.org/W2128484254","https://openalex.org/W2134815007","https://openalex.org/W2913093503","https://openalex.org/W3032347096","https://openalex.org/W3093323969","https://openalex.org/W3098935468","https://openalex.org/W3114734220","https://openalex.org/W3159719254","https://openalex.org/W4280543136","https://openalex.org/W4307230602","https://openalex.org/W4309858927","https://openalex.org/W4309908854","https://openalex.org/W4318978985","https://openalex.org/W4327550249","https://openalex.org/W4375858802","https://openalex.org/W4388464011","https://openalex.org/W4394578964","https://openalex.org/W4396918685"],"related_works":["https://openalex.org/W3104537585","https://openalex.org/W102940356","https://openalex.org/W2225560680","https://openalex.org/W2973523639","https://openalex.org/W4389309199","https://openalex.org/W2112585543","https://openalex.org/W2022374214","https://openalex.org/W4399694730","https://openalex.org/W2084743099","https://openalex.org/W2121688928"],"abstract_inverted_index":{"The":[0],"alignment":[1],"tool":[2],"is":[3,19,31],"part":[4],"of":[5],"the":[6,34,42],"RCSB":[7],"PDB":[8],"research-focused":[9],"RCSB.org":[10],"web":[11],"portal":[12],"and":[13,39],"available":[14,20],"at":[15,28],"rcsb.org/alignment.":[16],"Programmatic":[17],"access":[18],"via":[21],"alignment.rcsb.org.":[22],"Frontend":[23],"code":[24],"has":[25],"been":[26],"published":[27],"github.com/rcsb/rcsb-pecos-app.":[29],"Visualization":[30],"powered":[32],"by":[33],"open-source":[35],"Mol*":[36],"viewer":[37],"(github.com/molstar/molstar":[38],"github.com/molstar/rcsb-molstar)":[40],"plus":[41],"Sequence":[43],"Annotations":[44],"in":[45],"3D":[46],"Viewer":[47],"(github.com/rcsb/rcsb-saguaro-3d).":[48]},"counts_by_year":[{"year":2026,"cited_by_count":28},{"year":2025,"cited_by_count":126},{"year":2024,"cited_by_count":23}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}