{"id":"https://openalex.org/W4406408768","doi":"https://doi.org/10.1021/acs.jcim.4c01373","title":"PPDock: Pocket Prediction-Based Protein\u2013Ligand Blind Docking","display_name":"PPDock: Pocket Prediction-Based Protein\u2013Ligand Blind Docking","publication_year":2025,"publication_date":"2025-01-15","ids":{"openalex":"https://openalex.org/W4406408768","doi":"https://doi.org/10.1021/acs.jcim.4c01373","pmid":"https://pubmed.ncbi.nlm.nih.gov/39814581"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01373","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01373","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100594305","display_name":"Jie Du","orcid":null},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Du","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"],"raw_orcid":"https://orcid.org/0009-0003-0181-4823","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","institution_ids":["https://openalex.org/I133868755"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011879942","display_name":"Mingzhi Yuan","orcid":"https://orcid.org/0000-0003-1322-7530"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingzhi Yuan","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"],"raw_orcid":"https://orcid.org/0000-0003-1322-7530","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","institution_ids":["https://openalex.org/I133868755"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089201296","display_name":"Ao Shen","orcid":"https://orcid.org/0009-0001-1937-6855"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ao Shen","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"],"raw_orcid":"https://orcid.org/0009-0001-1937-6855","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","institution_ids":["https://openalex.org/I133868755"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029371371","display_name":"Manning Wang","orcid":"https://orcid.org/0000-0002-9255-3897"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Manning Wang","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-9255-3897","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China","institution_ids":["https://openalex.org/I133868755"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Shanghai 200032, P. R. China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5029371371"],"corresponding_institution_ids":["https://openalex.org/I133868755"],"apc_list":null,"apc_paid":null,"fwci":6.1977,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.96287651,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"65","issue":"2","first_page":"554","last_page":"562"},"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":0.9742000102996826,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.932200014591217,"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/docking","display_name":"Docking (animal)","score":0.9318820834159851},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.8304780721664429},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5810240507125854},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.5219566226005554},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5130597352981567},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.384345144033432},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.38346588611602783},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3676936626434326},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.27730172872543335},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.23295503854751587},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21813005208969116},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19517385959625244},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16423481702804565},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11763814091682434},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.06930229067802429}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.9318820834159851},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.8304780721664429},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5810240507125854},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.5219566226005554},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5130597352981567},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.384345144033432},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.38346588611602783},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3676936626434326},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.27730172872543335},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.23295503854751587},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21813005208969116},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19517385959625244},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16423481702804565},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11763814091682434},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.06930229067802429},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c01373","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01373","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39814581","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39814581","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7754111381","display_name":null,"funder_award_id":"23S41900400","funder_id":"https://openalex.org/F4320336652","funder_display_name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320336652","display_name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W569478347","https://openalex.org/W1583837637","https://openalex.org/W1653739410","https://openalex.org/W1985588649","https://openalex.org/W2020084080","https://openalex.org/W2028629022","https://openalex.org/W2044444984","https://openalex.org/W2050456292","https://openalex.org/W2067455153","https://openalex.org/W2067643341","https://openalex.org/W2108389384","https://openalex.org/W2134967712","https://openalex.org/W2214665483","https://openalex.org/W2244785476","https://openalex.org/W2343614482","https://openalex.org/W2587598315","https://openalex.org/W2768092025","https://openalex.org/W2804163281","https://openalex.org/W2909638144","https://openalex.org/W2914568473","https://openalex.org/W2949504121","https://openalex.org/W2975900595","https://openalex.org/W2978329087","https://openalex.org/W2990138404","https://openalex.org/W3168430821","https://openalex.org/W3177828909","https://openalex.org/W3199883166","https://openalex.org/W4220871410","https://openalex.org/W4281701642","https://openalex.org/W4285728205","https://openalex.org/W4306867651","https://openalex.org/W4327550249","https://openalex.org/W4388685549","https://openalex.org/W4389963497","https://openalex.org/W4392242468","https://openalex.org/W4402589989"],"related_works":["https://openalex.org/W1489925612","https://openalex.org/W3011103292","https://openalex.org/W4400485740","https://openalex.org/W2533022751","https://openalex.org/W2064383522","https://openalex.org/W2862730334","https://openalex.org/W2553094381","https://openalex.org/W2585040066","https://openalex.org/W2072180710","https://openalex.org/W2221759783"],"abstract_inverted_index":{"Predicting":[0],"the":[1,8,36,63,74],"docking":[2,22,34,42,56,90,108,135],"conformation":[3],"of":[4],"a":[5,25,88,105],"ligand":[6],"in":[7,32,79,128],"protein":[9,65],"binding":[10],"site":[11],"(pocket),":[12],"i.e.,":[13],"protein-ligand":[14],"docking,":[15,67],"is":[16,38,95],"crucial":[17],"for":[18,66],"drug":[19],"discovery.":[20],"Traditional":[21],"methods":[23,60,127],"have":[24,48],"long":[26],"inference":[27,51],"time":[28],"and":[29,53,77,139],"low":[30],"accuracy":[31],"blind":[33,41,107],"(when":[35],"pocket":[37,76,93,112],"unknown).":[39],"Recently,":[40],"techniques":[43],"based":[44,110],"on":[45,111,118],"deep":[46],"learning":[47],"significantly":[49],"improved":[50],"efficiency":[52],"achieved":[54],"good":[55],"results.":[57],"However,":[58],"these":[59],"often":[61],"use":[62],"entire":[64],"which":[68],"makes":[69],"it":[70],"difficult":[71],"to":[72],"identify":[73],"correct":[75],"results":[78],"poor":[80],"generalization":[81,137],"performance.":[82],"In":[83],"this":[84,101],"study,":[85],"we":[86,103],"propose":[87],"two-stage":[89],"paradigm,":[91,102],"where":[92],"prediction":[94,113],"followed":[96],"by":[97],"pocket-based":[98],"docking.":[99],"Following":[100],"design":[104],"new":[106],"method":[109],"(PPDock).":[114],"Through":[115],"extensive":[116],"experiments":[117],"benchmark":[119],"data":[120],"sets,":[121],"our":[122],"proposed":[123],"PPDock":[124],"outperforms":[125],"existing":[126],"nearly":[129],"all":[130],"evaluation":[131],"metrics,":[132],"demonstrating":[133],"strong":[134],"accuracy,":[136],"ability,":[138],"efficiency.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
