{"id":"https://openalex.org/W2217901364","doi":"https://doi.org/10.1021/ci6002202","title":"Use of Amino Acid Composition to Predict Ligand-Binding Sites","display_name":"Use of Amino Acid Composition to Predict Ligand-Binding Sites","publication_year":2007,"publication_date":"2007-01-23","ids":{"openalex":"https://openalex.org/W2217901364","doi":"https://doi.org/10.1021/ci6002202","mag":"2217901364","pmid":"https://pubmed.ncbi.nlm.nih.gov/17243757"},"language":"en","primary_location":{"id":"doi:10.1021/ci6002202","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci6002202","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/A5109103255","display_name":"Shinji Soga","orcid":null},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]},{"id":"https://openalex.org/I142395110","display_name":"Astellas Pharma (Japan)","ror":"https://ror.org/01cjash87","country_code":"JP","type":"company","lineage":["https://openalex.org/I142395110"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shinji Soga","raw_affiliation_strings":["Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan","institution_ids":["https://openalex.org/I1314466530","https://openalex.org/I142395110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111922082","display_name":"Hiroki Shirai","orcid":null},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]},{"id":"https://openalex.org/I142395110","display_name":"Astellas Pharma (Japan)","ror":"https://ror.org/01cjash87","country_code":"JP","type":"company","lineage":["https://openalex.org/I142395110"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroki Shirai","raw_affiliation_strings":["Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan","institution_ids":["https://openalex.org/I1314466530","https://openalex.org/I142395110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078990256","display_name":"Masato Kobori","orcid":null},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]},{"id":"https://openalex.org/I142395110","display_name":"Astellas Pharma (Japan)","ror":"https://ror.org/01cjash87","country_code":"JP","type":"company","lineage":["https://openalex.org/I142395110"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masato Kobori","raw_affiliation_strings":["Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan","institution_ids":["https://openalex.org/I1314466530","https://openalex.org/I142395110"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068719582","display_name":"N. Hirayama","orcid":"https://orcid.org/0000-0001-9288-6328"},"institutions":[{"id":"https://openalex.org/I1314466530","display_name":"Tokai University","ror":"https://ror.org/01p7qe739","country_code":"JP","type":"education","lineage":["https://openalex.org/I1314466530"]},{"id":"https://openalex.org/I142395110","display_name":"Astellas Pharma (Japan)","ror":"https://ror.org/01cjash87","country_code":"JP","type":"company","lineage":["https://openalex.org/I142395110"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Noriaki Hirayama","raw_affiliation_strings":["Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan, and Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan","institution_ids":["https://openalex.org/I1314466530","https://openalex.org/I142395110"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.8622,"has_fulltext":false,"cited_by_count":207,"citation_normalized_percentile":{"value":0.9721049,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"47","issue":"2","first_page":"400","last_page":"406"},"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":0.9995999932289124,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.7633095979690552},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.652752161026001},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6320836544036865},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5246303677558899},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.5067322850227356},{"id":"https://openalex.org/keywords/ligand-efficiency","display_name":"Ligand efficiency","score":0.49066054821014404},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.487439900636673},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4224736988544464},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35737740993499756},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3469785451889038},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3060261607170105},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21458178758621216},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.06531590223312378}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.7633095979690552},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.652752161026001},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6320836544036865},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5246303677558899},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.5067322850227356},{"id":"https://openalex.org/C204171352","wikidata":"https://www.wikidata.org/wiki/Q6545861","display_name":"Ligand efficiency","level":4,"score":0.49066054821014404},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.487439900636673},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4224736988544464},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35737740993499756},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3469785451889038},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3060261607170105},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21458178758621216},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.06531590223312378}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci6002202","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci6002202","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:17243757","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17243757","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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1541765387","https://openalex.org/W1585634379","https://openalex.org/W1973689805","https://openalex.org/W2007450175","https://openalex.org/W2033495141","https://openalex.org/W2055043387","https://openalex.org/W2076773887","https://openalex.org/W2090467197","https://openalex.org/W2091563009","https://openalex.org/W2103935162","https://openalex.org/W2126609920","https://openalex.org/W2130479394","https://openalex.org/W2151345203"],"related_works":["https://openalex.org/W3143642740","https://openalex.org/W4285478100","https://openalex.org/W1570348606","https://openalex.org/W2167226024","https://openalex.org/W2161203845","https://openalex.org/W2758868811","https://openalex.org/W2769265168","https://openalex.org/W4214840794","https://openalex.org/W2067323612","https://openalex.org/W2048470987"],"abstract_inverted_index":{"A":[0,39],"novel":[1,184],"method":[2],"for":[3,8,61,73,93],"predicting":[4],"the":[5,12,19,22,29,42,47,53,89,102,112,115,125,142,158,165,173],"binding":[6,54,75,92,99,159],"sites":[7,31,55,100,113,128,160,175,186],"druglike":[9,57,162],"compounds":[10],"on":[11,18,101],"surface":[13],"of":[14,21,32,44,46,56,65,91,133,161,176,187],"proteins":[15,103],"was":[16,59,77,85],"developed":[17],"basis":[20],"specific":[23],"amino":[24,50],"acid":[25],"composition":[26],"observed":[27],"at":[28,52,96],"ligand-binding":[30,155,174],"ligand-protein":[33],"complexes":[34],"determined":[35,107],"by":[36,108],"X-ray":[37,109],"analysis.":[38,110],"profile":[40],"representing":[41],"preference":[43],"each":[45],"20":[48],"standard":[49],"acids":[51],"molecules":[58],"obtained":[60],"a":[62,130],"small":[63],"set":[64],"high-quality":[66],"complex":[67],"structures.":[68],"An":[69],"index":[70,84,167],"termed":[71],"propensity":[72,90],"ligand":[74],"(PLB)":[76],"created":[78],"from":[79],"these":[80],"profiles.":[81],"The":[82,135],"PLB":[83,119,136,166],"used":[86,170],"to":[87,153,171,182],"predict":[88,172],"804":[94],"ligands":[95],"all":[97],"potential":[98],"whose":[104],"structures":[105,179],"were":[106],"If":[111],"with":[114],"first":[116],"two":[117],"highest":[118],"indices":[120],"are":[121],"taken":[122],"into":[123],"consideration,":[124],"successfully":[126],"predicted":[127],"reached":[129],"high":[131],"percentage":[132],"86.":[134],"prediction":[137],"is":[138,148],"relatively":[139],"simple,":[140],"but":[141],"validation":[143],"study":[144],"showed":[145],"that":[146],"it":[147],"both":[149],"fast":[150],"and":[151,180],"accurate":[152],"detect":[154],"sites,":[156],"especially":[157],"molecules.":[163],"Therefore,":[164],"can":[168],"be":[169],"uncharacterized":[177],"protein":[178],"also":[181],"identify":[183],"drug-binding":[185],"known":[188],"drug":[189],"targets.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":29},{"year":2020,"cited_by_count":25},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":6}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
