{"id":"https://openalex.org/W1980209352","doi":"https://doi.org/10.1021/ci700149k","title":"Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces","display_name":"Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces","publication_year":2007,"publication_date":"2007-09-27","ids":{"openalex":"https://openalex.org/W1980209352","doi":"https://doi.org/10.1021/ci700149k","mag":"1980209352","pmid":"https://pubmed.ncbi.nlm.nih.gov/17900106"},"language":"en","primary_location":{"id":"doi:10.1021/ci700149k","doi":"https://doi.org/10.1021/ci700149k","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci700149k","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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"},"volume":null,"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/A5008756376","display_name":"Shijun Zhong","orcid":"https://orcid.org/0000-0002-4213-2808","observed_orcids":["https://orcid.org/0000-0002-4213-2808"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shijun Zhong","raw_affiliation_strings":["Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056944006","display_name":"Alexander D. MacKerell","orcid":"https://orcid.org/0000-0001-8287-6804","observed_orcids":["https://orcid.org/0000-0001-8287-6804","https://orcid.org/0000-0003-4290-182X"]},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander D. MacKerell","raw_affiliation_strings":["Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201","institution_ids":["https://openalex.org/I126744593"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I126744593"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":5.4374,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.953677,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"47","issue":"6","first_page":"2303","last_page":"2315"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980000257492065,"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":0.9980000257492065,"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":0.0007999999797903001,"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/T11908","display_name":"Protein Interaction Studies and Fluorescence Analysis","score":0.0003000000142492354,"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/protein-ligand-interactions","display_name":"protein-ligand interactions","score":0.8489999771118164},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"virtual screening","score":0.5770000219345093},{"id":"https://openalex.org/keywords/probe-compounds","display_name":"probe compounds","score":0.6309999823570251},{"id":"https://openalex.org/keywords/binding-energy","display_name":"binding energy","score":0.8619999885559082},{"id":"https://openalex.org/keywords/site-clustering","display_name":"site clustering","score":0.6690000295639038},{"id":"https://openalex.org/keywords/de-novo-drug-design","display_name":"de novo drug design","score":0.8029999732971191},{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.703000009059906}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.6775240302085876},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6742817759513855},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.673526406288147},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.5877455472946167},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5580844879150391},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4916017949581146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4872521460056305},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.27321237325668335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24946117401123047},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2231946587562561},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0742357075214386},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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/ci700149k","doi":"https://doi.org/10.1021/ci700149k","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci700149k","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"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:17900106","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17900106","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,"listed_in":[],"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"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G6247186097","display_name":null,"funder_award_id":"CA 107331","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6444124784","display_name":"Substrate specific ERK docking domain inhibitors","funder_award_id":"R01CA120215","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7345209011","display_name":"Restoration of Tumor Suppression Activity in Malignant Melanoma","funder_award_id":"R01CA107331","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G855522446","display_name":null,"funder_award_id":"CA120215","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W631602627","https://openalex.org/W1493926273","https://openalex.org/W1541274513","https://openalex.org/W1571577887","https://openalex.org/W1585634379","https://openalex.org/W1592950931","https://openalex.org/W1965220003","https://openalex.org/W1975293246","https://openalex.org/W1977698783","https://openalex.org/W1980549837","https://openalex.org/W1981824495","https://openalex.org/W1991745348","https://openalex.org/W1994801829","https://openalex.org/W1995497226","https://openalex.org/W2000295215","https://openalex.org/W2017345038","https://openalex.org/W2027408247","https://openalex.org/W2029667189","https://openalex.org/W2030860488","https://openalex.org/W2031772330","https://openalex.org/W2038147869","https://openalex.org/W2043699100","https://openalex.org/W2046548222","https://openalex.org/W2050470003","https://openalex.org/W2059491946","https://openalex.org/W2063831812","https://openalex.org/W2066143642","https://openalex.org/W2066638035","https://openalex.org/W2067074955","https://openalex.org/W2067455153","https://openalex.org/W2071791280","https://openalex.org/W2082040139","https://openalex.org/W2091981413","https://openalex.org/W2097420030","https://openalex.org/W2098971704","https://openalex.org/W2104760790","https://openalex.org/W2105438341","https://openalex.org/W2108508060","https://openalex.org/W2115592403","https://openalex.org/W2117744495","https://openalex.org/W2126311442","https://openalex.org/W2127445307","https://openalex.org/W2128402268","https://openalex.org/W2128421003","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2134427214","https://openalex.org/W2135732933","https://openalex.org/W2136513242","https://openalex.org/W2137134615","https://openalex.org/W2140407975","https://openalex.org/W2144062946","https://openalex.org/W2145113008","https://openalex.org/W2152477898","https://openalex.org/W2158534713","https://openalex.org/W2162166182","https://openalex.org/W2200017991","https://openalex.org/W2318777851","https://openalex.org/W2419340920"],"related_works":["https://openalex.org/W7106299991","https://openalex.org/W2128402268","https://openalex.org/W2973743369","https://openalex.org/W2090794687","https://openalex.org/W4416907357","https://openalex.org/W2168580221","https://openalex.org/W4404226808","https://openalex.org/W6999404959","https://openalex.org/W2806017263","https://openalex.org/W2587559223"],"abstract_inverted_index":{"The":[0,63,122],"identification":[1,179,190],"of":[2,16,18,53,60,71,82,88,116,124,135,156,191],"ligand":[3,102,107],"binding":[4,29,36,48,64,83,93,98,103,146,192],"sites":[5,49,99,147,193],"on":[6,50,68,194],"a":[7,32,57,86,133],"protein":[8],"is":[9,38,66,95,127,174],"an":[10,185],"essential":[11],"step":[12],"in":[13,40,118,153,159],"the":[14,35,41,51,69,75,80,110,114,119,140,144,149,160,167,189],"selection":[15],"inhibitors":[17],"protein-ligand":[19,137],"or":[20,200],"protein-protein":[21],"interactions":[22],"via":[23],"virtual":[24],"database":[25,87,198],"screening.":[26],"To":[27],"facilitate":[28],"site":[30,112,152,178],"identification,":[31],"novel":[33],"descriptor,":[34],"response,":[37],"proposed":[39],"present":[42],"paper":[43],"to":[44,56,132,142,183],"quantitatively":[45],"evaluate":[46],"putative":[47,111],"basis":[52,70],"their":[54],"response":[55,65,94],"test":[58,89,120],"set":[59],"probe":[61],"compounds.":[62],"determined":[67],"contributions":[72],"from":[73],"both":[74],"ligand-protein":[76],"interaction":[77],"energy":[78],"and":[79,105,180],"geometry":[81],"poses":[84],"for":[85,97,113,188,197],"ligands.":[90],"A":[91],"favorable":[92,101],"obtained":[96],"with":[100,106,176],"energies":[104],"geometries":[108],"within":[109],"majority":[115],"compounds":[117],"set.":[121],"utility":[123],"this":[125],"descriptor":[126],"illustrated":[128],"by":[129],"applying":[130],"it":[131,164],"number":[134],"known":[136],"complexes,":[138],"showing":[139],"approach":[141,187],"identify":[143],"experimental":[145],"as":[148],"highest":[150],"scoring":[151,170],"26":[154],"out":[155],"29":[157],"cases;":[158],"remaining":[161],"three":[162,169],"cases,":[163],"was":[165],"among":[166],"top":[168],"sites.":[171],"This":[172],"method":[173],"combined":[175],"sphere-based":[177],"clustering":[181],"methods":[182],"yield":[184],"automated":[186],"proteins":[195],"suitable":[196],"screen":[199],"de":[201],"novo":[202],"drug":[203],"design.":[204]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":6}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}