{"id":"https://openalex.org/W4390588971","doi":"https://doi.org/10.1186/s12859-023-05586-5","title":"Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data","display_name":"Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data","publication_year":2024,"publication_date":"2024-01-04","ids":{"openalex":"https://openalex.org/W4390588971","doi":"https://doi.org/10.1186/s12859-023-05586-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/38177985"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05586-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05586-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05586-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05586-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068604431","display_name":"Eli J. Draizen","orcid":"https://orcid.org/0000-0002-5645-5050"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eli J. Draizen","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. edraizen@gmail.com","School of Data Science, University of Virginia, Charlottesville, VA, USA. edraizen@gmail.com","Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. edraizen@gmail.com","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"School of Data Science, University of Virginia, Charlottesville, VA, USA. edraizen@gmail.com","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073372312","display_name":"John Readey","orcid":null},"institutions":[{"id":"https://openalex.org/I4210108985","display_name":"Bellevue Hospital Center","ror":"https://ror.org/01ky34z31","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283621791","https://openalex.org/I4210086933","https://openalex.org/I4210108985"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Readey","raw_affiliation_strings":["The HDF Group, Bellevue, WA, USA"],"affiliations":[{"raw_affiliation_string":"The HDF Group, Bellevue, WA, USA","institution_ids":["https://openalex.org/I4210108985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022761529","display_name":"Cameron Mura","orcid":"https://orcid.org/0000-0001-7985-2561"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cameron Mura","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. cmura@virginia.edu","School of Data Science, University of Virginia, Charlottesville, VA, USA. cmura@virginia.edu","Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. cmura@virginia.edu","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"School of Data Science, University of Virginia, Charlottesville, VA, USA. cmura@virginia.edu","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip E. Bourne","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","School of Data Science, University of Virginia, Charlottesville, VA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"School of Data Science, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5068604431"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7369,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.67920274,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"11","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9966999888420105,"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":0.9966999888420105,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9966999888420105,"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":0.9965000152587891,"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/python","display_name":"Python (programming language)","score":0.9020524024963379},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6263587474822998},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3770439326763153},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3578230142593384},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3440623879432678},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3294077515602112},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.329384982585907},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3260398507118225},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18550068140029907}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9020524024963379},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6263587474822998},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3770439326763153},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3578230142593384},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3440623879432678},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3294077515602112},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.329384982585907},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3260398507118225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18550068140029907}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05586-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05586-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05586-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38177985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38177985","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10768222","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10768222","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10768222/pdf/12859_2023_Article_5586.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c6bda3fd57b8472a998f3e96bcf243a3","is_oa":true,"landing_page_url":"https://doaj.org/article/c6bda3fd57b8472a998f3e96bcf243a3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-24 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05586-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05586-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05586-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G164679396","display_name":null,"funder_award_id":"Presidential Fellowship","funder_id":"https://openalex.org/F4320310536","funder_display_name":"University of Virginia"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310536","display_name":"University of Virginia","ror":"https://ror.org/0153tk833"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4390588971.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1533059251","https://openalex.org/W1607931568","https://openalex.org/W1966127665","https://openalex.org/W1975304761","https://openalex.org/W1993715180","https://openalex.org/W2001900040","https://openalex.org/W2008708467","https://openalex.org/W2017382438","https://openalex.org/W2025859600","https://openalex.org/W2026593599","https://openalex.org/W2030841140","https://openalex.org/W2070318172","https://openalex.org/W2098718123","https://openalex.org/W2102245393","https://openalex.org/W2106648157","https://openalex.org/W2111472630","https://openalex.org/W2124241917","https://openalex.org/W2131417105","https://openalex.org/W2138104170","https://openalex.org/W2158714788","https://openalex.org/W2165565773","https://openalex.org/W2185628700","https://openalex.org/W2253581743","https://openalex.org/W2302501749","https://openalex.org/W2539190955","https://openalex.org/W2604075160","https://openalex.org/W2607211817","https://openalex.org/W2613409207","https://openalex.org/W2617750324","https://openalex.org/W2731784911","https://openalex.org/W2800648160","https://openalex.org/W2890223884","https://openalex.org/W2913820882","https://openalex.org/W2949223833","https://openalex.org/W2950192635","https://openalex.org/W2952811294","https://openalex.org/W2973136764","https://openalex.org/W3005364306","https://openalex.org/W3033096976","https://openalex.org/W3095435122","https://openalex.org/W3104537585","https://openalex.org/W3106745904","https://openalex.org/W3112376646","https://openalex.org/W3112468720","https://openalex.org/W3125756628","https://openalex.org/W3134089816","https://openalex.org/W3162801148","https://openalex.org/W3163595068","https://openalex.org/W3176355504","https://openalex.org/W3177828909","https://openalex.org/W3211795435","https://openalex.org/W3216616254","https://openalex.org/W3217314753","https://openalex.org/W4200477411","https://openalex.org/W4211196614","https://openalex.org/W4289334206","https://openalex.org/W4296032638","https://openalex.org/W4296098995","https://openalex.org/W4309862248","https://openalex.org/W4311181469","https://openalex.org/W4327550249","https://openalex.org/W4402596898","https://openalex.org/W6634119514","https://openalex.org/W6786423766"],"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/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
