{"id":"https://openalex.org/W2233270115","doi":"https://doi.org/10.1021/acs.jcim.5b00625","title":"Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein\u2013Ligand Binding Prediction in CSAR 2013 and 2014","display_name":"Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein\u2013Ligand Binding Prediction in CSAR 2013 and 2014","publication_year":2015,"publication_date":"2015-12-22","ids":{"openalex":"https://openalex.org/W2233270115","doi":"https://doi.org/10.1021/acs.jcim.5b00625","mag":"2233270115","pmid":"https://pubmed.ncbi.nlm.nih.gov/26691286"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00625","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00625","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/A5084858860","display_name":"Xiaolei Zhu","orcid":"https://orcid.org/0000-0002-1967-2806"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xiaolei Zhu","raw_affiliation_strings":["Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States","School\rof Life Science, Anhui University, Hefei, Anhui 230601, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"School\rof Life Science, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040488997","display_name":"Woong\u2010Hee Shin","orcid":"https://orcid.org/0000-0003-3462-0243"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Woong-Hee Shin","raw_affiliation_strings":["Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066751552","display_name":"Hyungrae Kim","orcid":"https://orcid.org/0000-0002-2617-6288"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyungrae Kim","raw_affiliation_strings":["Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062293219","display_name":"Daisuke Kihara","orcid":"https://orcid.org/0000-0003-4091-6614"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daisuke Kihara","raw_affiliation_strings":["Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States","Department\rof Computer Science, Purdue University, West Lafayette, Indiana 47907, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biology Science, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Department\rof Computer Science, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062293219"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":2.0183,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.87864133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"56","issue":"6","first_page":"1088","last_page":"1099"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9986000061035156,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.996399998664856,"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/ligand","display_name":"Ligand (biochemistry)","score":0.5063480138778687},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45918363332748413},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44064462184906006},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.35335367918014526},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29429104924201965},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.15257832407951355},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15134698152542114}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5063480138778687},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45918363332748413},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44064462184906006},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35335367918014526},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29429104924201965},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.15257832407951355},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15134698152542114}],"mesh":[{"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":"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","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":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5b00625","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00625","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:26691286","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26691286","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:4328935","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5005040","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G156165454","display_name":null,"funder_award_id":"DBI-1262189","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G1765126292","display_name":"Identification of protein-metabolite interactome.","funder_award_id":"5r01gm097528-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2879580723","display_name":null,"funder_award_id":"IIS1319551","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"},{"id":"https://openalex.org/G7154359157","display_name":null,"funder_award_id":"IOS-1127027","funder_id":"https://openalex.org/F4320337399","funder_display_name":"Division of Integrative Organismal Systems"},{"id":"https://openalex.org/G718781169","display_name":null,"funder_award_id":"R01GM097528)","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7710527896","display_name":null,"funder_award_id":"21403002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"},{"id":"https://openalex.org/F4320337399","display_name":"Division of Integrative Organismal Systems","ror":"https://ror.org/01rvays47"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1592950931","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1688073391","https://openalex.org/W1974885083","https://openalex.org/W1979954275","https://openalex.org/W1982246455","https://openalex.org/W1984030577","https://openalex.org/W1988437166","https://openalex.org/W1993403967","https://openalex.org/W2002044972","https://openalex.org/W2003356525","https://openalex.org/W2003668179","https://openalex.org/W2012084558","https://openalex.org/W2021750784","https://openalex.org/W2028609644","https://openalex.org/W2042572511","https://openalex.org/W2065283382","https://openalex.org/W2067732724","https://openalex.org/W2070741080","https://openalex.org/W2071557543","https://openalex.org/W2072728308","https://openalex.org/W2076779488","https://openalex.org/W2078374001","https://openalex.org/W2086361102","https://openalex.org/W2087007556","https://openalex.org/W2105527266","https://openalex.org/W2105668062","https://openalex.org/W2111143975","https://openalex.org/W2113149246","https://openalex.org/W2118233996","https://openalex.org/W2119114829","https://openalex.org/W2121895929","https://openalex.org/W2123356345","https://openalex.org/W2126677834","https://openalex.org/W2128332459","https://openalex.org/W2132262459","https://openalex.org/W2134967712","https://openalex.org/W2158360182","https://openalex.org/W2169678694","https://openalex.org/W2214858482","https://openalex.org/W2236779797","https://openalex.org/W2249451730","https://openalex.org/W2270302232","https://openalex.org/W2337273834","https://openalex.org/W2364255377","https://openalex.org/W2417432242","https://openalex.org/W2440823401"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"The":[0,66],"Community":[1],"Structure-Activity":[2],"Resource":[3],"(CSAR)":[4],"benchmark":[5,46],"exercise":[6],"provides":[7],"a":[8],"unique":[9],"opportunity":[10],"for":[11,28,69,107,155],"researchers":[12],"to":[13,81,119,157,172],"objectively":[14],"evaluate":[15],"the":[16,84,103,146,151,192],"performance":[17,183],"of":[18,32,98,191],"protein-ligand":[19],"docking":[20],"methods.":[21],"Patch-Surfer":[22,78],"and":[23,44,123,133,187],"PL-PatchSurfer,":[24],"molecular":[25],"surface-based":[26],"methods":[27,179,193],"predicting":[29],"binding":[30,87,121],"ligands":[31,117,156],"proteins":[33,88],"developed":[34],"in":[35,48,61,73,115,124,129,145,184,196],"our":[36,178],"group,":[37],"were":[38],"tested":[39],"on":[40],"both":[41],"CSAR":[42,62,74,185],"2013":[43,63,75,130,186],"2014":[45,134,147],"exercises":[47],"combination":[49],"with":[50,163,198],"an":[51],"empirical":[52],"scoring":[53],"function-based":[54],"method,":[55],"AutoDock,":[56],"while":[57],"we":[58],"only":[59],"participated":[60],"using":[64],"Patch-Surfer.":[65],"prediction":[67],"results":[68,173],"Phase":[70,96,131,135,148],"1":[71],"task":[72],"showed":[76,141,180],"that":[77],"was":[79,168],"able":[80],"rank":[82],"all":[83],"four":[85],"designed":[86],"within":[89],"top":[90],"ranks,":[91],"outperforming":[92],"AutoDock":[93,139],"Vina.":[94],"In":[95],"2":[97,149],"2013,":[99],"PL-PatchSurfer":[100,111,152],"correctly":[101],"selected":[102],"correct":[104],"ligand":[105,127],"pose":[106],"two":[108],"target":[109,158],"proteins.":[110],"performed":[112],"reasonably":[113],"well":[114,162],"ranking":[116],"according":[118],"their":[120,164],"affinity":[122],"selecting":[125],"near-native":[126],"poses":[128],"3":[132],"1,":[136],"respectively,":[137],"although":[138],"Vina":[140],"better":[142,169],"performance.":[143],"Lastly,":[144],"exercise,":[150],"scores":[153],"computed":[154],"protein":[159],"pairs":[160],"correlated":[161],"pIC50":[165],"values,":[166],"which":[167],"or":[170],"comparable":[171],"by":[174],"other":[175],"participants.":[176],"Overall,":[177],"fairly":[181],"good":[182],"2014.":[188],"Unique":[189],"characteristics":[190],"are":[194],"discussed":[195],"comparison":[197],"AutoDock.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
