{"id":"https://openalex.org/W4399437600","doi":"https://doi.org/10.1186/s13321-024-00865-6","title":"PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction","display_name":"PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction","publication_year":2024,"publication_date":"2024-06-07","ids":{"openalex":"https://openalex.org/W4399437600","doi":"https://doi.org/10.1186/s13321-024-00865-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/38849917"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-024-00865-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00865-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00865-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00865-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030235824","display_name":"Kandel Jeevan","orcid":null},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Kandel Jeevan","raw_affiliation_strings":["Graduate School of Integrated Energy-AI, Jeonbuk National University, Jeonju, 54896, South Korea"],"affiliations":[{"raw_affiliation_string":"Graduate School of Integrated Energy-AI, Jeonbuk National University, Jeonju, 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099050045","display_name":"Shrestha Palistha","orcid":null},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Shrestha Palistha","raw_affiliation_strings":["Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008953921","display_name":"Hilal Tayara","orcid":"https://orcid.org/0000-0001-5678-3479"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hilal Tayara","raw_affiliation_strings":["School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea. hilaltayara@jbnu.ac.kr","School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea"],"affiliations":[{"raw_affiliation_string":"School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea. hilaltayara@jbnu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031342322","display_name":"Kil To Chong","orcid":"https://orcid.org/0000-0002-1952-0001"},"institutions":[{"id":"https://openalex.org/I80611190","display_name":"Jeonbuk National University","ror":"https://ror.org/05q92br09","country_code":"KR","type":"education","lineage":["https://openalex.org/I80611190"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kil T. Chong","raw_affiliation_strings":["Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","Graduate School of Integrated Energy-AI, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea"],"affiliations":[{"raw_affiliation_string":"Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Graduate School of Integrated Energy-AI, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"School of International Engineering and Science, Jeonbuk National University, Jeonju, 54896, South Korea. kitchong@jbnu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, 54896, South Korea","institution_ids":["https://openalex.org/I80611190"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5030235824"],"corresponding_institution_ids":["https://openalex.org/I80611190"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":6.6141,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.97245256,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"16","issue":"1","first_page":"66","last_page":"66"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9887999892234802,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9855999946594238,"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":0.6997988224029541},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5811635851860046},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5144789218902588},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45622166991233826},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4267016053199768},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.42363521456718445},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4194572865962982},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3356410562992096},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24184346199035645}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6997988224029541},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5811635851860046},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5144789218902588},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45622166991233826},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4267016053199768},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.42363521456718445},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4194572865962982},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3356410562992096},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24184346199035645},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-024-00865-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00865-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00865-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:38849917","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38849917","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11157904","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11157904","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11157904/pdf/13321_2024_Article_865.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:3156ae56aece40bd9a0eb50a2df23f1e","is_oa":true,"landing_page_url":"https://doaj.org/article/3156ae56aece40bd9a0eb50a2df23f1e","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":"Journal of Cheminformatics, Vol 16, Iss 1, Pp 1-16 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-024-00865-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00865-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00865-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1265821442","display_name":null,"funder_award_id":"106004","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G2082489056","display_name":null,"funder_award_id":"20204010600470","funder_id":"https://openalex.org/F4320335199","funder_display_name":"Korea Institute of Energy Technology Evaluation and Planning"},{"id":"https://openalex.org/G4069871152","display_name":null,"funder_award_id":"2020R1A2C2005612","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G4205419206","display_name":null,"funder_award_id":"2020R1A2C2005612","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G5943277139","display_name":null,"funder_award_id":"20204010600470","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G6073835783","display_name":null,"funder_award_id":"2020R1A2C2005612","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G936863556","display_name":null,"funder_award_id":"20204010600470","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335199","display_name":"Korea Institute of Energy Technology Evaluation and Planning","ror":"https://ror.org/02zq38y32"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399437600.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1901129140","https://openalex.org/W1980969309","https://openalex.org/W1982264103","https://openalex.org/W2011703027","https://openalex.org/W2018661561","https://openalex.org/W2031194866","https://openalex.org/W2058463742","https://openalex.org/W2077776336","https://openalex.org/W2081201773","https://openalex.org/W2090649877","https://openalex.org/W2090794687","https://openalex.org/W2091563009","https://openalex.org/W2109872885","https://openalex.org/W2114162221","https://openalex.org/W2114326383","https://openalex.org/W2116703791","https://openalex.org/W2128402268","https://openalex.org/W2130479394","https://openalex.org/W2140538197","https://openalex.org/W2144258433","https://openalex.org/W2150444353","https://openalex.org/W2164088236","https://openalex.org/W2169678694","https://openalex.org/W2194775991","https://openalex.org/W2617750324","https://openalex.org/W2734349601","https://openalex.org/W2887981960","https://openalex.org/W2918335507","https://openalex.org/W2949676527","https://openalex.org/W2955341169","https://openalex.org/W2963125977","https://openalex.org/W2963351448","https://openalex.org/W3005669732","https://openalex.org/W3034357529","https://openalex.org/W3096387236","https://openalex.org/W3165143074","https://openalex.org/W3197082762","https://openalex.org/W4225774159","https://openalex.org/W4226381600","https://openalex.org/W4229031603","https://openalex.org/W4317831504","https://openalex.org/W6891805465"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W4230611425","https://openalex.org/W2731899572","https://openalex.org/W2062195135","https://openalex.org/W4294635752","https://openalex.org/W4304166257","https://openalex.org/W4383066092","https://openalex.org/W3215138031","https://openalex.org/W4380075502"],"abstract_inverted_index":{"Accurate":[0],"ligand":[1],"binding":[2,79],"site":[3,80],"prediction":[4],"(LBSP)":[5],"within":[6],"proteins":[7],"is":[8],"essential":[9],"for":[10,102,111],"drug":[11,113],"discovery.":[12,114],"We":[13],"developed":[14],"ProteinUNetResNetV2.0":[15],"(PUResNetV2.0),":[16],"leveraging":[17],"sparse":[18,97],"representation":[19,98],"of":[20,96],"protein":[21,31,35],"structures":[22],"to":[23,85],"improve":[24],"LBSP":[25],"accuracy.":[26],"Our":[27,91],"training":[28,89],"dataset":[29],"included":[30],"complexes":[32],"from":[33],"4729":[34],"families.":[36],"Evaluations":[37],"on":[38,58],"benchmark":[39],"datasets":[40],"showed":[41],"that":[42],"PUResNetV2.0":[43,106],"achieved":[44],"an":[45],"85.4%":[46],"Distance":[47],"Center":[48],"Atom":[49],"(DCA)":[50],"success":[51],"rate":[52],"and":[53,77],"a":[54,108],"74.7%":[55],"F1":[56],"Score":[57],"the":[59,94],"Holo801":[60],"dataset,":[61],"outperforming":[62],"existing":[63],"methods.":[64],"However,":[65],"its":[66],"performance":[67],"in":[68,87,99],"specific":[69],"cases,":[70],"such":[71],"as":[72,107],"RNA,":[73],"DNA,":[74],"peptide-like":[75],"ligand,":[76],"ion":[78],"prediction,":[81],"was":[82],"limited":[83],"due":[84],"constraints":[86],"our":[88],"data.":[90],"findings":[92],"underscore":[93],"potential":[95],"LBSP,":[100],"especially":[101],"oligomeric":[103],"structures,":[104],"suggesting":[105],"promising":[109],"tool":[110],"computational":[112]},"counts_by_year":[{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
