{"id":"https://openalex.org/W2617750324","doi":"https://doi.org/10.1093/bioinformatics/btx350","title":"DeepSite: protein-binding site predictor using 3D-convolutional neural networks","display_name":"DeepSite: protein-binding site predictor using 3D-convolutional neural networks","publication_year":2017,"publication_date":"2017-05-30","ids":{"openalex":"https://openalex.org/W2617750324","doi":"https://doi.org/10.1093/bioinformatics/btx350","mag":"2617750324","pmid":"https://pubmed.ncbi.nlm.nih.gov/28575181"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx350","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/19/3036/25164841/btx350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/19/3036/25164841/btx350.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100700305","display_name":"Jos\u00e9 Jim\u00e9nez-Luna","orcid":"https://orcid.org/0000-0002-5335-7834"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"J Jim\u00e9nez","raw_affiliation_strings":["Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671","https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026884193","display_name":"Stefan Doerr","orcid":"https://orcid.org/0000-0002-8678-8657"},"institutions":[{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"S Doerr","raw_affiliation_strings":["Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671","https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054926156","display_name":"Gerard Mart\u00ednez-Rosell","orcid":"https://orcid.org/0000-0001-6277-6769"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"G Mart\u00ednez-Rosell","raw_affiliation_strings":["Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671","https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033139813","display_name":"Alexander Rose","orcid":"https://orcid.org/0000-0002-0893-5551"},"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"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A S Rose","raw_affiliation_strings":["San Diego Supercomputer Center, UC San Diego, MC 0505, 9500 Gilman Drive, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, UC San Diego, MC 0505, 9500 Gilman Drive, La Jolla, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027026045","display_name":"Gianni De Fabritiis","orcid":"https://orcid.org/0000-0003-3913-4877"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Pompeu Fabra University","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"G De Fabritiis","raw_affiliation_strings":["Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain","ICREA, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671","https://openalex.org/I170486558"]},{"raw_affiliation_string":"ICREA, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027026045"],"corresponding_institution_ids":["https://openalex.org/I11932220","https://openalex.org/I170486558","https://openalex.org/I2801864671"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":28.4419,"has_fulltext":true,"cited_by_count":816,"citation_normalized_percentile":{"value":0.99793195,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"33","issue":"19","first_page":"3036","last_page":"3042"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.996999979019165,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9842000007629395,"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":0.7646780014038086},{"id":"https://openalex.org/keywords/druggability","display_name":"Druggability","score":0.7587751150131226},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7204498648643494},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6701174378395081},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47021248936653137},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4355800449848175},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.42559707164764404},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.42385134100914},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3698974847793579},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3548390567302704},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22070211172103882},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15180283784866333},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09304434061050415},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09067511558532715}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7646780014038086},{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.7587751150131226},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7204498648643494},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6701174378395081},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47021248936653137},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4355800449848175},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.42559707164764404},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.42385134100914},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3698974847793579},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3548390567302704},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22070211172103882},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15180283784866333},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09304434061050415},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09067511558532715},{"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/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.0}],"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":"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx350","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/19/3036/25164841/btx350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28575181","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28575181","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx350","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/19/3036/25164841/btx350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5458998604","display_name":null,"funder_award_id":"BIO2014-53095-P","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320321595","display_name":"Federaci\u00f3n Espa\u00f1ola de Enfermedades Raras","ror":"https://ror.org/0348bpk17"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2617750324.pdf","grobid_xml":"https://content.openalex.org/works/W2617750324.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W199384682","https://openalex.org/W1517566065","https://openalex.org/W1623006543","https://openalex.org/W1806891645","https://openalex.org/W1980969309","https://openalex.org/W1997655258","https://openalex.org/W2019951137","https://openalex.org/W2031194866","https://openalex.org/W2058463742","https://openalex.org/W2067191022","https://openalex.org/W2069152576","https://openalex.org/W2078176948","https://openalex.org/W2091563009","https://openalex.org/W2105668062","https://openalex.org/W2132395520","https://openalex.org/W2145339207","https://openalex.org/W2161072217","https://openalex.org/W2164088236","https://openalex.org/W2296686360","https://openalex.org/W2502949459","https://openalex.org/W2557283755","https://openalex.org/W6636749155","https://openalex.org/W6638520917","https://openalex.org/W6682093823"],"related_works":["https://openalex.org/W2556855892","https://openalex.org/W4280541024","https://openalex.org/W4214810602","https://openalex.org/W2000687555","https://openalex.org/W1573015311","https://openalex.org/W2259552966","https://openalex.org/W2158546283","https://openalex.org/W2255897055","https://openalex.org/W4307035489","https://openalex.org/W2391481219"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":32},{"year":2025,"cited_by_count":140},{"year":2024,"cited_by_count":196},{"year":2023,"cited_by_count":120},{"year":2022,"cited_by_count":107},{"year":2021,"cited_by_count":101},{"year":2020,"cited_by_count":61},{"year":2019,"cited_by_count":38},{"year":2018,"cited_by_count":19},{"year":2017,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
