{"id":"https://openalex.org/W2954483845","doi":"https://doi.org/10.1021/acs.jcim.9b00445","title":"CoDockPP: A Multistage Approach for Global and Site-Specific Protein\u2013Protein Docking","display_name":"CoDockPP: A Multistage Approach for Global and Site-Specific Protein\u2013Protein Docking","publication_year":2019,"publication_date":"2019-07-05","ids":{"openalex":"https://openalex.org/W2954483845","doi":"https://doi.org/10.1021/acs.jcim.9b00445","mag":"2954483845","pmid":"https://pubmed.ncbi.nlm.nih.gov/31276391"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00445","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00445","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/A5043750371","display_name":"Ren Kong","orcid":"https://orcid.org/0000-0001-9010-1750"},"institutions":[{"id":"https://openalex.org/I4210144214","display_name":"Jiangsu University of Technology","ror":"https://ror.org/04jabhf80","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210144214"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ren Kong","raw_affiliation_strings":["Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China","institution_ids":["https://openalex.org/I4210144214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078138911","display_name":"Feng Wang","orcid":"https://orcid.org/0000-0002-0275-8267"},"institutions":[{"id":"https://openalex.org/I4210144214","display_name":"Jiangsu University of Technology","ror":"https://ror.org/04jabhf80","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210144214"]},{"id":"https://openalex.org/I4210153482","display_name":"Changzhou University","ror":"https://ror.org/04ymgwq66","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210153482"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Wang","raw_affiliation_strings":["Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China","School of Information Science & Engineering, Changzhou University, Changzhou 213164, China"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China","institution_ids":["https://openalex.org/I4210144214"]},{"raw_affiliation_string":"School of Information Science & Engineering, Changzhou University, Changzhou 213164, China","institution_ids":["https://openalex.org/I4210153482"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100409987","display_name":"Jian Zhang","orcid":"https://orcid.org/0000-0002-6558-791X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Zhang","raw_affiliation_strings":["Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China"],"affiliations":[{"raw_affiliation_string":"Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101563333","display_name":"Fengfei Wang","orcid":"https://orcid.org/0000-0003-3423-211X"},"institutions":[{"id":"https://openalex.org/I4210144214","display_name":"Jiangsu University of Technology","ror":"https://ror.org/04jabhf80","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210144214"]},{"id":"https://openalex.org/I4210153482","display_name":"Changzhou University","ror":"https://ror.org/04ymgwq66","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210153482"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fengfei Wang","raw_affiliation_strings":["Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China","School of Information Science & Engineering, Changzhou University, Changzhou 213164, China"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China","institution_ids":["https://openalex.org/I4210144214"]},{"raw_affiliation_string":"School of Information Science & Engineering, Changzhou University, Changzhou 213164, China","institution_ids":["https://openalex.org/I4210153482"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071710594","display_name":"Shan Chang","orcid":"https://orcid.org/0000-0001-7169-9398"},"institutions":[{"id":"https://openalex.org/I4210144214","display_name":"Jiangsu University of Technology","ror":"https://ror.org/04jabhf80","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210144214"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shan Chang","raw_affiliation_strings":["Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China"],"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China","institution_ids":["https://openalex.org/I4210144214"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5071710594"],"corresponding_institution_ids":["https://openalex.org/I4210144214"],"apc_list":null,"apc_paid":null,"fwci":4.7905,"has_fulltext":false,"cited_by_count":47,"citation_normalized_percentile":{"value":0.95407727,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"59","issue":"8","first_page":"3556","last_page":"3564"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9987000226974487,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9797000288963318,"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":0.8267751932144165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6614081263542175},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.5721693634986877},{"id":"https://openalex.org/keywords/fast-fourier-transform","display_name":"Fast Fourier transform","score":0.503680408000946},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.47315797209739685},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.4729692041873932},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3712034225463867},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3155110478401184},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3015875816345215},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.2080429494380951},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17626330256462097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1448785364627838}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8267751932144165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6614081263542175},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.5721693634986877},{"id":"https://openalex.org/C75172450","wikidata":"https://www.wikidata.org/wiki/Q623950","display_name":"Fast Fourier transform","level":2,"score":0.503680408000946},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.47315797209739685},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.4729692041873932},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3712034225463867},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3155110478401184},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3015875816345215},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2080429494380951},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17626330256462097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1448785364627838},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"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/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00445","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00445","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:31276391","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31276391","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/G3467644355","display_name":null,"funder_award_id":"81603152","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5762864255","display_name":null,"funder_award_id":"2016-XYDXXJS-020","funder_id":"https://openalex.org/F4320321605","funder_display_name":"Government of Jiangsu Province"},{"id":"https://openalex.org/G6806602780","display_name":null,"funder_award_id":"BY2016030-11","funder_id":"https://openalex.org/F4320321605","funder_display_name":"Government of Jiangsu Province"},{"id":"https://openalex.org/G7621048702","display_name":null,"funder_award_id":"BY2016030-06","funder_id":"https://openalex.org/F4320321605","funder_display_name":"Government of Jiangsu Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1030883578","https://openalex.org/W1194601030","https://openalex.org/W1545810434","https://openalex.org/W1658199422","https://openalex.org/W1711872148","https://openalex.org/W1965410913","https://openalex.org/W1993951624","https://openalex.org/W1999232134","https://openalex.org/W2000383223","https://openalex.org/W2006905684","https://openalex.org/W2010068428","https://openalex.org/W2019691413","https://openalex.org/W2036000659","https://openalex.org/W2054394841","https://openalex.org/W2055905702","https://openalex.org/W2083734879","https://openalex.org/W2090160089","https://openalex.org/W2091734240","https://openalex.org/W2096259534","https://openalex.org/W2099907934","https://openalex.org/W2102182691","https://openalex.org/W2105668062","https://openalex.org/W2111397525","https://openalex.org/W2118517681","https://openalex.org/W2132629607","https://openalex.org/W2133712572","https://openalex.org/W2136777954","https://openalex.org/W2137167381","https://openalex.org/W2137885918","https://openalex.org/W2137890647","https://openalex.org/W2140522686","https://openalex.org/W2153255725","https://openalex.org/W2153983456","https://openalex.org/W2155008097","https://openalex.org/W2158071704","https://openalex.org/W2158534713","https://openalex.org/W2160868144","https://openalex.org/W2163462520","https://openalex.org/W2164059036","https://openalex.org/W2164255317","https://openalex.org/W2165531467","https://openalex.org/W2169562071","https://openalex.org/W2171249995","https://openalex.org/W2333639763","https://openalex.org/W2334483166","https://openalex.org/W2436513885","https://openalex.org/W2465190302","https://openalex.org/W2465234710","https://openalex.org/W2514282803","https://openalex.org/W2615136515","https://openalex.org/W2616561032","https://openalex.org/W2738931202","https://openalex.org/W2753374271","https://openalex.org/W2767509030","https://openalex.org/W2794368672","https://openalex.org/W2887788718","https://openalex.org/W2891149559","https://openalex.org/W2952711759"],"related_works":["https://openalex.org/W2057846043","https://openalex.org/W2336040088","https://openalex.org/W2208175234","https://openalex.org/W1987493370","https://openalex.org/W3187431608","https://openalex.org/W1974422922","https://openalex.org/W2078688023","https://openalex.org/W2163614321","https://openalex.org/W4309353019","https://openalex.org/W4247206618"],"abstract_inverted_index":{"Protein-protein":[0],"docking":[1,64,85,157,187,203],"technology":[2],"is":[3,46,213],"an":[4],"effective":[5],"approach":[6,27],"to":[7,48,102,118,142,148,217],"study":[8],"the":[9,33,38,50,60,67,95,99,104,119,124,145,154,159,165,178,193],"molecular":[10],"mechanism":[11],"of":[12,69,94,98,126,156],"essential":[13],"biological":[14],"processes":[15],"mediated":[16],"by":[17,177],"complex":[18],"protein-protein":[19,42,84,186],"interactions.":[20],"The":[21,113,211],"fast":[22],"Fourier":[23],"transform":[24],"(FFT)":[25],"correlation":[26],"makes":[28],"a":[29,82,135,149],"good":[30,110],"balance":[31],"between":[32],"exhaustive":[34],"global":[35,72],"sampling":[36,73,96,167],"and":[37,55,74,129,134,169,196,204,215],"computational":[39],"efficiency":[40,97],"for":[41,123],"docking.":[43],"However,":[44],"it":[45],"difficult":[47,209],"integrate":[49],"precise":[51,75,179],"knowledge-based":[52,180],"scoring":[53,76,139,181],"function":[54],"site":[56,127],"constraint":[57],"information":[58],"into":[59],"FFT-based":[61,100],"approach.":[62],"New":[63],"strategies":[65],"with":[66,109,220],"capability":[68],"combining":[70],"both":[71,200],"are":[77,116,140,163,174],"strongly":[78],"needed.":[79],"We":[80],"propose":[81],"multistage":[83],"strategy":[86],"called":[87],"CoDockPP.":[88],"This":[89],"program":[90],"takes":[91],"full":[92],"advantage":[93],"method":[101],"choose":[103],"valid":[105],"ligand":[106],"protein":[107],"poses":[108,115,147,173],"surface":[111],"complementarity.":[112],"retained":[114],"transformed":[117],"real":[120],"Cartesian":[121],"space":[122],"implementation":[125],"constraints":[128,133],"atomic":[130],"scoring.":[131],"Site":[132],"rapid":[136],"table":[137],"lookup":[138],"applied":[141],"gradually":[143],"reduce":[144],"candidate":[146],"tractable":[150],"number.":[151],"To":[152],"enhance":[153],"accuracy":[155],"prediction,":[158],"best":[160],"fast-scoring":[161],"states":[162],"expanded":[164],"local":[166],"points":[168],"then":[170],"these":[171],"neighbor":[172],"further":[175],"evaluated":[176],"function.":[182],"By":[183],"testing":[184],"on":[185],"benchmark":[188],"5.0,":[189],"CoDockPP":[190],"remarkably":[191],"improves":[192],"success":[194],"rate":[195],"hit":[197],"count":[198],"in":[199,208],"<i>ab":[201],"initio</i>":[202],"site-specific":[205],"docking,":[206],"especially":[207],"cases.":[210],"server":[212],"free":[214],"open":[216],"all":[218],"users":[219],"no":[221],"login":[222],"requirement":[223],"at":[224],"http://codockpp.schanglab.org.cn":[225],".":[226]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":10}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}