{"id":"https://openalex.org/W4404092056","doi":"https://doi.org/10.1093/bioinformatics/btae654","title":"Afpdb: an efficient structure manipulation package for AI protein design","display_name":"Afpdb: an efficient structure manipulation package for AI protein design","publication_year":2024,"publication_date":"2024-11-05","ids":{"openalex":"https://openalex.org/W4404092056","doi":"https://doi.org/10.1093/bioinformatics/btae654","pmid":"https://pubmed.ncbi.nlm.nih.gov/39499140"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae654","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae654/60428073/btae654.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/btae654/60428073/btae654.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108384814","display_name":"Yingyao Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]},{"id":"https://openalex.org/I92507152","display_name":"John Jay College of Criminal Justice","ror":"https://ror.org/01p9rc392","country_code":"US","type":"education","lineage":["https://openalex.org/I92507152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yingyao Zhou","raw_affiliation_strings":["Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA"],"affiliations":[{"raw_affiliation_string":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","institution_ids":["https://openalex.org/I127128434"]},{"raw_affiliation_string":"Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA","institution_ids":["https://openalex.org/I127128434","https://openalex.org/I92507152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103976607","display_name":"J. Ricky Cox","orcid":null},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]},{"id":"https://openalex.org/I92507152","display_name":"John Jay College of Criminal Justice","ror":"https://ror.org/01p9rc392","country_code":"US","type":"education","lineage":["https://openalex.org/I92507152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiayi Cox","raw_affiliation_strings":["Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA"],"affiliations":[{"raw_affiliation_string":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","institution_ids":["https://openalex.org/I127128434"]},{"raw_affiliation_string":"Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA","institution_ids":["https://openalex.org/I127128434","https://openalex.org/I92507152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107748482","display_name":"Bin Zhou","orcid":"https://orcid.org/0000-0002-5879-5614"},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]},{"id":"https://openalex.org/I92507152","display_name":"John Jay College of Criminal Justice","ror":"https://ror.org/01p9rc392","country_code":"US","type":"education","lineage":["https://openalex.org/I92507152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bin Zhou","raw_affiliation_strings":["Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA"],"affiliations":[{"raw_affiliation_string":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","institution_ids":["https://openalex.org/I127128434"]},{"raw_affiliation_string":"Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA","institution_ids":["https://openalex.org/I127128434","https://openalex.org/I92507152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076847781","display_name":"Steven Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210144809","display_name":"Project Walk Paralysis Recovery Centers","ror":"https://ror.org/04ead8931","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210144809"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Zhu","raw_affiliation_strings":["Metascape Foundation , Carlsbad, CA 92009,","Metascape Foundation, Carlsbad, CA 92009, USA"],"affiliations":[{"raw_affiliation_string":"Metascape Foundation , Carlsbad, CA 92009,","institution_ids":["https://openalex.org/I4210144809"]},{"raw_affiliation_string":"Metascape Foundation, Carlsbad, CA 92009, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060039147","display_name":"Zhong Yang","orcid":"https://orcid.org/0000-0002-9146-0875"},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]},{"id":"https://openalex.org/I92507152","display_name":"John Jay College of Criminal Justice","ror":"https://ror.org/01p9rc392","country_code":"US","type":"education","lineage":["https://openalex.org/I92507152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Zhong","raw_affiliation_strings":["Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA"],"affiliations":[{"raw_affiliation_string":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","institution_ids":["https://openalex.org/I127128434"]},{"raw_affiliation_string":"Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA","institution_ids":["https://openalex.org/I127128434","https://openalex.org/I92507152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016539643","display_name":"Glen Spraggon","orcid":"https://orcid.org/0000-0001-7880-8454"},"institutions":[{"id":"https://openalex.org/I127128434","display_name":"Genomics Institute of the Novartis Research Foundation","ror":"https://ror.org/017136v53","country_code":"US","type":"facility","lineage":["https://openalex.org/I127128434","https://openalex.org/I1283582996","https://openalex.org/I4210117619"]},{"id":"https://openalex.org/I92507152","display_name":"John Jay College of Criminal Justice","ror":"https://ror.org/01p9rc392","country_code":"US","type":"education","lineage":["https://openalex.org/I92507152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Glen Spraggon","raw_affiliation_strings":["Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA"],"affiliations":[{"raw_affiliation_string":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","institution_ids":["https://openalex.org/I127128434"]},{"raw_affiliation_string":"Novartis Biomedical Research, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA","institution_ids":["https://openalex.org/I127128434","https://openalex.org/I92507152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5108384814"],"corresponding_institution_ids":["https://openalex.org/I127128434","https://openalex.org/I92507152"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17762824,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"40","issue":"12","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":0.9829999804496765,"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":0.9829999804496765,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.98089998960495,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.972599983215332,"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/computer-science","display_name":"Computer science","score":0.8582171201705933},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5888780355453491},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5868262648582458},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5811846852302551},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4948040843009949},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4898371398448944},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4846085011959076},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.43708330392837524},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.40584975481033325},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2608400583267212},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20260784029960632}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8582171201705933},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5888780355453491},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5868262648582458},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5811846852302551},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4948040843009949},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4898371398448944},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4846085011959076},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.43708330392837524},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.40584975481033325},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2608400583267212},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20260784029960632},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae654","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae654/60428073/btae654.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:39499140","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39499140","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:11631506","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11631506","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11631506/pdf/btae654.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/btae654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae654","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae654/60428073/btae654.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":[{"id":"https://metadata.un.org/sdg/8","score":0.46000000834465027,"display_name":"Decent work and economic growth"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404092056.pdf","grobid_xml":"https://content.openalex.org/works/W4404092056.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W2114850508","https://openalex.org/W2116389515","https://openalex.org/W2123681603","https://openalex.org/W2130479394","https://openalex.org/W2151581834","https://openalex.org/W2168172687","https://openalex.org/W2170711116","https://openalex.org/W2621473099","https://openalex.org/W2801127413","https://openalex.org/W2952811294","https://openalex.org/W3177828909","https://openalex.org/W4229042017","https://openalex.org/W4281790889","https://openalex.org/W4296032638","https://openalex.org/W4379383636","https://openalex.org/W4383957026","https://openalex.org/W4389167075","https://openalex.org/W4390154657","https://openalex.org/W4392544734","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W2341953792","https://openalex.org/W2789551765"],"abstract_inverted_index":{"Code":[0],"and":[1,8],"documentation":[2],"are":[3],"available":[4],"on":[5],"GitHub":[6],"(https://github.com/data2code/afpdb)":[7],"PyPI":[9],"(https://pypi.org/project/afpdb).":[10],"An":[11],"interactive":[12],"tutorial":[13],"is":[14],"accessible":[15],"through":[16],"Google":[17],"Colab.":[18]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
