{"id":"https://openalex.org/W2076022099","doi":"https://doi.org/10.1186/1471-2105-11-193","title":"A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction","display_name":"A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction","publication_year":2010,"publication_date":"2010-04-17","ids":{"openalex":"https://openalex.org/W2076022099","doi":"https://doi.org/10.1186/1471-2105-11-193","mag":"2076022099","pmid":"https://pubmed.ncbi.nlm.nih.gov/20398404"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-193","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-193","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-193.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-193.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071322222","display_name":"Tiejun Cheng","orcid":"https://orcid.org/0000-0002-4486-3356"},"institutions":[{"id":"https://openalex.org/I4210112946","display_name":"Shanghai Institute of Organic Chemistry","ror":"https://ror.org/01y3hvq34","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tiejun Cheng","raw_affiliation_strings":["State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, PR China","institution_ids":["https://openalex.org/I4210112946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100753007","display_name":"Zhihai Liu","orcid":"https://orcid.org/0000-0002-4527-8829"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112946","display_name":"Shanghai Institute of Organic Chemistry","ror":"https://ror.org/01y3hvq34","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihai Liu","raw_affiliation_strings":["State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, PR, China","State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, PR, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]},{"raw_affiliation_string":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016374232","display_name":"Renxiao Wang","orcid":"https://orcid.org/0000-0003-0485-0259"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112946","display_name":"Shanghai Institute of Organic Chemistry","ror":"https://ror.org/01y3hvq34","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Renxiao Wang","raw_affiliation_strings":["State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, PR, China","State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, PR, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112946"]},{"raw_affiliation_string":"State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016374232"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112946"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.5546,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.89233066,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"11","issue":"1","first_page":"193","last_page":"193"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7049999833106995,"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":0.7049999833106995,"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":0.1599999964237213,"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":0.01860000006854534,"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":0.5500067472457886},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5102040767669678},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4983632564544678},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39680615067481995},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3442806601524353},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33703240752220154},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3212846517562866},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18521398305892944},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10837256908416748},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07504525780677795}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5500067472457886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5102040767669678},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4983632564544678},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39680615067481995},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3442806601524353},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33703240752220154},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3212846517562866},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18521398305892944},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10837256908416748},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07504525780677795},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-193","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-193","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-193.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20398404","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20398404","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:1919540","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2868011","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:676016b12c35430cafc8083cb953d2dc","is_oa":false,"landing_page_url":"https://doaj.org/article/676016b12c35430cafc8083cb953d2dc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 193 (2010)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-193","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-193","pdf_url":"https://link.springer.com/content/pdf/10.1186/1471-2105-11-193.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.7400000095367432,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G2883361222","display_name":null,"funder_award_id":"2009ZX09501","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"}],"funders":[{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2076022099.pdf","grobid_xml":"https://content.openalex.org/works/W2076022099.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W659454094","https://openalex.org/W1505394602","https://openalex.org/W1573009101","https://openalex.org/W1592950931","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1964640150","https://openalex.org/W1967897381","https://openalex.org/W1970658820","https://openalex.org/W1972148009","https://openalex.org/W1973191530","https://openalex.org/W1974809008","https://openalex.org/W1975580333","https://openalex.org/W1975606737","https://openalex.org/W1977467384","https://openalex.org/W1983304433","https://openalex.org/W1984021058","https://openalex.org/W1985588649","https://openalex.org/W1988111902","https://openalex.org/W1992787746","https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W2003356525","https://openalex.org/W2004102775","https://openalex.org/W2007212378","https://openalex.org/W2011230643","https://openalex.org/W2012084558","https://openalex.org/W2017448415","https://openalex.org/W2020388373","https://openalex.org/W2039350725","https://openalex.org/W2040617462","https://openalex.org/W2042071104","https://openalex.org/W2043429268","https://openalex.org/W2047509756","https://openalex.org/W2048207135","https://openalex.org/W2050456292","https://openalex.org/W2051163038","https://openalex.org/W2053503396","https://openalex.org/W2053759741","https://openalex.org/W2061079400","https://openalex.org/W2061800084","https://openalex.org/W2066787645","https://openalex.org/W2071447504","https://openalex.org/W2074978477","https://openalex.org/W2076965051","https://openalex.org/W2085564033","https://openalex.org/W2092285329","https://openalex.org/W2096729078","https://openalex.org/W2098971704","https://openalex.org/W2102377211","https://openalex.org/W2105527266","https://openalex.org/W2107506448","https://openalex.org/W2114779636","https://openalex.org/W2115318272","https://openalex.org/W2116007667","https://openalex.org/W2118587156","https://openalex.org/W2121895929","https://openalex.org/W2128332459","https://openalex.org/W2130479394","https://openalex.org/W2132786452","https://openalex.org/W2158360182","https://openalex.org/W2158534713","https://openalex.org/W2160916136","https://openalex.org/W2163498131","https://openalex.org/W2168045053","https://openalex.org/W2169562071","https://openalex.org/W2187578091","https://openalex.org/W2204075485","https://openalex.org/W2211224366","https://openalex.org/W2213601517","https://openalex.org/W2949243165","https://openalex.org/W4250830547"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2961085424","https://openalex.org/W2150084125","https://openalex.org/W1802639773","https://openalex.org/W2118505788","https://openalex.org/W1972196578","https://openalex.org/W1490878237","https://openalex.org/W1542823905","https://openalex.org/W2990314835"],"abstract_inverted_index":{"BACKGROUND:":[0],"Current":[1],"scoring":[2,26,162,223,237,279],"functions":[3,163,280],"are":[4],"not":[5,215,229,243],"very":[6],"successful":[7],"in":[8,16,106,113,158,255,285],"protein-ligand":[9,43,66,93,107,134,264],"binding":[10,38,49,70,108,120,265,286],"affinity":[11,287],"prediction":[12,117],"albeit":[13],"their":[14,283],"popularity":[15],"structure-based":[17],"drug":[18],"designs.":[19],"Here,":[20],"we":[21],"propose":[22],"a":[23,41,62,88,114,137,146,273],"general":[24],"knowledge-guided":[25],"(KGS)":[27],"strategy":[28,35,155,203,227,253,269],"to":[29,73,86,95,149,220,245,258,281],"tackle":[30],"this":[31],"problem.":[32],"Our":[33,153,185,267],"KGS":[34,154,202,226,252,268],"computes":[36],"the":[37,47,78,98,142,150,201,259],"constant":[39,50],"of":[40,51,65,91,97,100,118,200,250,262],"given":[42],"complex":[44,83,99,144],"based":[45],"on":[46,167,188,235],"known":[48,69],"an":[52,126],"appropriate":[53],"reference":[54,79,82,143],"complex.":[55,80,152],"A":[56],"good":[57],"training":[58],"set":[59],"that":[60,96,198],"includes":[61],"sufficient":[63],"number":[64],"complexes":[67],"with":[68,145,160],"data":[71],"needs":[72],"be":[74],"supplied":[75],"for":[76,131,277],"finding":[77],"The":[81,248],"is":[84,242,254],"required":[85],"share":[87],"similar":[89],"pattern":[90],"key":[92,133],"interactions":[94,135],"interest.":[101],"Thus,":[102],"some":[103],"uncertain":[104],"factors":[105],"may":[109,270],"cancel":[110],"out,":[111],"resulting":[112],"more":[115,205,274],"accurate":[116,206],"absolute":[119],"constants.":[121],"RESULTS:":[122],"In":[123],"our":[124,225,251],"study,":[125],"automatic":[127],"algorithm":[128],"was":[129,156],"developed":[130],"summarizing":[132],"as":[136,191,193,272],"pharmacophore":[138],"model":[139],"and":[140,165,180,239],"identifying":[141],"maximal":[147],"similarity":[148],"query":[151],"evaluated":[157],"combination":[159],"two":[161],"(X-Score":[164],"PLP)":[166],"three":[168],"test":[169],"sets,":[170],"containing":[171],"112":[172],"HIV":[173],"protease":[174],"complexes,":[175,179,183],"44":[176],"carbonic":[177],"anhydrase":[178],"73":[181],"trypsin":[182],"respectively.":[184],"results":[186],"obtained":[187],"crystal":[189],"structures":[190],"well":[192],"computer-generated":[194],"docking":[195],"poses":[196],"indicated":[197],"application":[199,241],"produced":[204],"predictions":[207],"especially":[208],"when":[209],"X-Score":[210],"or":[211,233],"PLP":[212],"alone":[213],"did":[214],"perform":[216],"well.":[217],"CONCLUSIONS:":[218],"Compared":[219],"other":[221],"targeted":[222],"functions,":[224],"does":[228],"require":[230],"any":[231],"re-parameterization":[232],"modification":[234],"current":[236,278],"methods,":[238],"its":[240],"tied":[244],"certain":[246],"systems.":[247],"effectiveness":[249],"theory":[256],"proportional":[257],"ever-increasing":[260],"knowledge":[261],"experimental":[263],"data.":[266],"serve":[271],"practical":[275],"remedy":[276],"improve":[282],"accuracy":[284],"prediction.":[288]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}