{"id":"https://openalex.org/W2051562942","doi":"https://doi.org/10.1021/ci200501p","title":"Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors","display_name":"Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors","publication_year":2012,"publication_date":"2012-04-03","ids":{"openalex":"https://openalex.org/W2051562942","doi":"https://doi.org/10.1021/ci200501p","mag":"2051562942","pmid":"https://pubmed.ncbi.nlm.nih.gov/22471323"},"language":"en","primary_location":{"id":"doi:10.1021/ci200501p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200501p","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/A5111756846","display_name":"Jong Young Joung","orcid":null},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Jong Young Joung","raw_affiliation_strings":["Bioinformatics & Molecular Design Research Center, Seoul 120-749, Republic of Korea","Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Bioinformatics & Molecular Design Research Center, Seoul 120-749, Republic of Korea","institution_ids":[]},{"raw_affiliation_string":"Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106083710","display_name":"Ky-Youb Nam","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ky-Youb Nam","raw_affiliation_strings":["Bioinformatics & Molecular Design Research Center, Seoul 120-749, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Bioinformatics & Molecular Design Research Center, Seoul 120-749, Republic of Korea","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114256881","display_name":"Kwang-Hwi Cho","orcid":null},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kwang-Hwi Cho","raw_affiliation_strings":["School of Systems Biomedical Science and CAMD Research Center, Soongsil University, Seoul 156-743, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"School of Systems Biomedical Science and CAMD Research Center, Soongsil University, Seoul 156-743, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055744835","display_name":"Kyoung Tai No","orcid":"https://orcid.org/0000-0003-3187-8193"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyoung Tai No","raw_affiliation_strings":["Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea","Translational Research Center for Protein Function Control, Seoul 120-749, Republic of Korea","Department#R#of Biotechnology, Yonsei University, Seoul#R#120-749, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]},{"raw_affiliation_string":"Translational Research Center for Protein Function Control, Seoul 120-749, Republic of Korea","institution_ids":[]},{"raw_affiliation_string":"Department#R#of Biotechnology, Yonsei University, Seoul#R#120-749, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5111756846"],"corresponding_institution_ids":["https://openalex.org/I193775966"],"apc_list":null,"apc_paid":null,"fwci":0.3369,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.61304191,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"52","issue":"4","first_page":"984","last_page":"995"},"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":0.9976000189781189,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9736999869346619,"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/conformational-isomerism","display_name":"Conformational isomerism","score":0.7428052425384521},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.5971115231513977},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5910537838935852},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5219753980636597},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5160550475120544},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3955440819263458},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.39452487230300903},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3660139739513397},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.2599623203277588}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.7428052425384521},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.5971115231513977},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5910537838935852},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5219753980636597},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5160550475120544},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3955440819263458},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.39452487230300903},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3660139739513397},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2599623203277588},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"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},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","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":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200501p","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200501p","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:22471323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22471323","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":[{"score":0.8700000047683716,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W776218354","https://openalex.org/W1536742834","https://openalex.org/W1592950931","https://openalex.org/W1973523623","https://openalex.org/W1983304433","https://openalex.org/W1985588649","https://openalex.org/W1987930291","https://openalex.org/W1988437166","https://openalex.org/W1992681077","https://openalex.org/W1995379006","https://openalex.org/W2011630732","https://openalex.org/W2014252980","https://openalex.org/W2014704001","https://openalex.org/W2032646124","https://openalex.org/W2037970873","https://openalex.org/W2050456292","https://openalex.org/W2051543023","https://openalex.org/W2052030759","https://openalex.org/W2056626791","https://openalex.org/W2057846043","https://openalex.org/W2061766994","https://openalex.org/W2063531028","https://openalex.org/W2067397351","https://openalex.org/W2068017935","https://openalex.org/W2078889865","https://openalex.org/W2081719547","https://openalex.org/W2087256237","https://openalex.org/W2089442765","https://openalex.org/W2089989874","https://openalex.org/W2092285329","https://openalex.org/W2108001390","https://openalex.org/W2111340290","https://openalex.org/W2114779636","https://openalex.org/W2116244477","https://openalex.org/W2129157803","https://openalex.org/W2147856316","https://openalex.org/W2158534713","https://openalex.org/W2161634702","https://openalex.org/W2216566030","https://openalex.org/W4213077798","https://openalex.org/W4253859701"],"related_works":["https://openalex.org/W2023036309","https://openalex.org/W1972863456","https://openalex.org/W2089371831","https://openalex.org/W2052399476","https://openalex.org/W2810163160","https://openalex.org/W3083970380","https://openalex.org/W2037964119","https://openalex.org/W4220905048","https://openalex.org/W4385077663","https://openalex.org/W838464343"],"abstract_inverted_index":{"To":[0],"reduce":[1],"searching":[2],"effort":[3],"in":[4,23,133,201],"conformational":[5],"space":[6,111],"of":[7,20,42,48,63,98,118,125,128,140,161,165,189,204],"ligand":[8,22,55,66,99,105],"docking":[9],"positions,":[10],"we":[11,86,136],"propose":[12],"an":[13,70],"algorithm":[14],"that":[15,115],"generates":[16],"initial":[17,61,74],"binding":[18],"positions":[19,100],"the":[21,29,33,39,54,57,60,109,116,123,138,141,153,159,173,184,202,207],"a":[24,64],"target":[25],"protein,":[26],"based":[27],"on":[28],"property-weighted":[30],"vector":[31,36],"(P-weiV),":[32],"three-dimensional":[34,89],"orthogonal":[35,90],"determined":[37],"by":[38,79],"molecular":[40],"property":[41],"hydration-free":[43],"energy":[44,81],"density.":[45],"The":[46],"alignment":[47,160],"individual":[49],"P-weiVs":[50],"calculated":[51],"separately":[52],"for":[53,103,172,183],"and":[56,178,197],"protein":[58],"gives":[59],"orientation":[62],"given":[65],"conformation":[67],"relative":[68],"to":[69,92,122,144,194],"active":[71],"site;":[72],"these":[73],"orientations":[75,97],"are":[76,87,101],"then":[77],"ranked":[78,176,187],"simple":[80],"functions,":[82],"including":[83],"solvation.":[84],"Because":[85],"using":[88],"vectors":[91],"be":[93],"aligned,":[94],"only":[95],"four":[96],"possible":[102],"each":[104],"conformation,":[106],"which":[107],"reduces":[108],"search":[110],"dramatically.":[112],"We":[113],"found":[114],"performance":[117],"P-weiV":[119,156],"compared":[120,193],"favorably":[121],"use":[124],"principle":[126],"moment":[127],"inertia":[129],"(PMI)":[130],"as":[131,192],"implemented":[132],"LigandFit":[134],"when":[135],"tested":[137],"abilities":[139],"two":[142],"approaches":[143],"correctly":[145,157],"predict":[146],"205":[147],"protein-ligand":[148],"complex":[149],"data":[150],"sets":[151],"from":[152],"PDBBind":[154],"database.":[155],"predicted":[158],"ligands":[162],"(within":[163],"rmsd":[164],"2.5":[166],"\u00c5)":[167],"with":[168,179,206],"57.6%":[169],"reliability":[170,181],"(118/205)":[171],"top":[174,185],"10":[175],"conformations":[177,188],"74.1%":[180],"(152/205)":[182],"50":[186],"Catalyst-generated":[190],"conformers,":[191],"22.9%":[195],"(47/205)":[196],"31.2%":[198],"(64/205),":[199],"respectively,":[200],"case":[203],"PMI":[205],"same":[208],"conformer":[209],"set.":[210]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}