{"id":"https://openalex.org/W2090035064","doi":"https://doi.org/10.1021/ci8004308","title":"Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?","display_name":"Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?","publication_year":2009,"publication_date":"2009-05-15","ids":{"openalex":"https://openalex.org/W2090035064","doi":"https://doi.org/10.1021/ci8004308","mag":"2090035064","pmid":"https://pubmed.ncbi.nlm.nih.gov/19445499"},"language":"en","primary_location":{"id":"doi:10.1021/ci8004308","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci8004308","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/A5033668564","display_name":"Pablo Englebienne","orcid":null},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Pablo Englebienne","raw_affiliation_strings":["Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, Canada H3A 2K6","Department of Chemistry, McGill University, 801 Sherbrooke St. W. Montreal, Quebec, Canada, H3A 2K6"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, Canada H3A 2K6","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Chemistry, McGill University, 801 Sherbrooke St. W. Montreal, Quebec, Canada, H3A 2K6","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035012955","display_name":"Nicolas Moitessier","orcid":"https://orcid.org/0000-0001-6933-2079"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nicolas Moitessier","raw_affiliation_strings":["Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, Canada H3A 2K6","Department of Chemistry, McGill University, 801 Sherbrooke St. W. Montreal, Quebec, Canada, H3A 2K6"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec, Canada H3A 2K6","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"Department of Chemistry, McGill University, 801 Sherbrooke St. W. Montreal, Quebec, Canada, H3A 2K6","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033668564"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":null,"apc_paid":null,"fwci":16.0663,"has_fulltext":false,"cited_by_count":84,"citation_normalized_percentile":{"value":0.99518578,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"49","issue":"6","first_page":"1568","last_page":"1580"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9983999729156494,"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":0.9887999892234802,"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/macromolecule","display_name":"Macromolecule","score":0.7796051502227783},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.6046704649925232},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5646408200263977},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5166097283363342},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.500697135925293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4446335434913635},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.3277057409286499},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2710394859313965},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23757800459861755},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22417834401130676},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13445985317230225}],"concepts":[{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.7796051502227783},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.6046704649925232},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5646408200263977},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5166097283363342},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.500697135925293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4446335434913635},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3277057409286499},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2710394859313965},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23757800459861755},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22417834401130676},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13445985317230225},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci8004308","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci8004308","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:19445499","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19445499","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":[{"display_name":"Clean water and sanitation","score":0.8500000238418579,"id":"https://metadata.un.org/sdg/6"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1512801428","https://openalex.org/W1573009101","https://openalex.org/W1605578858","https://openalex.org/W1963775782","https://openalex.org/W1972148009","https://openalex.org/W1975304761","https://openalex.org/W1977467384","https://openalex.org/W1981608946","https://openalex.org/W1982441109","https://openalex.org/W1983143653","https://openalex.org/W1983194490","https://openalex.org/W1984021058","https://openalex.org/W1985588649","https://openalex.org/W1992583240","https://openalex.org/W1993046136","https://openalex.org/W2001816314","https://openalex.org/W2010663744","https://openalex.org/W2012084558","https://openalex.org/W2020040806","https://openalex.org/W2037963167","https://openalex.org/W2044573154","https://openalex.org/W2052030759","https://openalex.org/W2053418558","https://openalex.org/W2053603003","https://openalex.org/W2072569763","https://openalex.org/W2086787941","https://openalex.org/W2089887872","https://openalex.org/W2092285329","https://openalex.org/W2111893205","https://openalex.org/W2115318272","https://openalex.org/W2118587156","https://openalex.org/W2128332459","https://openalex.org/W2130479394","https://openalex.org/W2135817448","https://openalex.org/W2146015083","https://openalex.org/W2152964937","https://openalex.org/W2160916136"],"related_works":["https://openalex.org/W2044014390","https://openalex.org/W1846316342","https://openalex.org/W1964725291","https://openalex.org/W4210447090","https://openalex.org/W1984670152","https://openalex.org/W2083665351","https://openalex.org/W2043468722","https://openalex.org/W2123419409","https://openalex.org/W2003172604","https://openalex.org/W2768531357"],"abstract_inverted_index":{"In":[0],"our":[1],"previous":[2],"report,":[3],"we":[4,29,50],"investigated":[5],"the":[6,12,18,35,42,83,86,90,136,150,161,170,183,192,200,207],"impact":[7,36],"of":[8,14,21,34,37,44,54,59,68,89,141,160],"protein":[9,76,172],"flexibility":[10],"and":[11,74,93,123,138,149,206],"presence":[13],"water":[15,72,184],"molecules":[16,73,185],"on":[17,41,199],"pose-prediction":[19],"accuracy":[20,43,118,140,211],"major":[22,98],"docking":[23],"programs.":[24],"To":[25,47],"complete":[26],"these":[27,38,107],"investigations,":[28],"report":[30],"herein":[31],"a":[32,65,97],"study":[33,134,178],"two":[39,52],"aspects":[40],"scoring":[45,111,152,163,187,204],"functions.":[46],"this":[48,195],"effect,":[49],"developed":[51],"sets":[53],"protein/ligand":[55],"complexes":[56],"made":[57,80],"up":[58],"ligands":[60,92],"cross-docked":[61],"or":[62],"cocrystallized":[63,131],"with":[64],"large":[66],"variety":[67],"proteins,":[69],"featuring":[70],"bridging":[71],"demonstrating":[75],"flexibility.":[77],"Efforts":[78],"were":[79,165],"to":[81,119,124,130],"reduce":[82],"correlation":[84,202],"between":[85,203],"molecular":[87],"weights":[88],"selected":[91],"their":[94,117,128],"binding":[95,121],"affinities,":[96],"bias":[99],"in":[100,210],"some":[101],"previously":[102],"reported":[103],"benchmark":[104],"sets.":[105],"Using":[106],"sets,":[108],"18":[109],"available":[110],"functions":[112,164,205],"have":[113],"been":[114],"assessed":[115,162],"for":[116,186],"predict":[120],"affinities":[122],"rank-order":[125],"compounds":[126],"by":[127],"affinity":[129],"proteins.":[132],"This":[133,177],"confirmed":[135],"good":[137],"similar":[139],"Xscore,":[142],"GlideScore,":[143],"DrugScore(CSD),":[144],"GoldScore,":[145],"PLP1,":[146],"ChemScore,":[147],"RankScore,":[148],"eHiTS":[151],"function.":[153],"Our":[154],"next":[155],"investigations":[156],"demonstrated":[157],"that":[158,181],"most":[159],"much":[166],"less":[167],"accurate":[168],"when":[169],"correct":[171],"conformation":[173],"was":[174],"not":[175,189],"provided.":[176],"also":[179],"revealed":[180],"considering":[182],"does":[188],"greatly":[190],"affect":[191],"accuracy.":[193],"Finally,":[194],"work":[196],"sheds":[197],"light":[198],"high":[201],"poor":[208],"increase":[209],"one":[212],"can":[213],"expect":[214],"from":[215],"consensus":[216],"scoring.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":14}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}