{"id":"https://openalex.org/W2394671537","doi":"https://doi.org/10.1021/acs.jcim.5b00158","title":"Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function","display_name":"Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function","publication_year":2015,"publication_date":"2015-09-29","ids":{"openalex":"https://openalex.org/W2394671537","doi":"https://doi.org/10.1021/acs.jcim.5b00158","mag":"2394671537","pmid":"https://pubmed.ncbi.nlm.nih.gov/26418299"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00158","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00158","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/A5014949338","display_name":"A. Y. Lizunov","orcid":null},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]},{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"A. Y. Lizunov","raw_affiliation_strings":["Department\rof Mathematics, Moscow Institute of Physics and Technology, Moscow 117303, Russia","Faculty\rof Fundamental Medicine, Moscow State University, Moscow 119991, Russia"],"affiliations":[{"raw_affiliation_string":"Department\rof Mathematics, Moscow Institute of Physics and Technology, Moscow 117303, Russia","institution_ids":["https://openalex.org/I153845743"]},{"raw_affiliation_string":"Faculty\rof Fundamental Medicine, Moscow State University, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086205409","display_name":"A. L. Gonchar","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"A. L. Gonchar","raw_affiliation_strings":["Faculty\rof Fundamental Medicine, Moscow State University, Moscow 119991, Russia"],"affiliations":[{"raw_affiliation_string":"Faculty\rof Fundamental Medicine, Moscow State University, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010866774","display_name":"\u041d. \u0418. \u0417\u0430\u0439\u0446\u0435\u0432\u0430","orcid":null},"institutions":[{"id":"https://openalex.org/I17877952","display_name":"Sechenov University","ror":"https://ror.org/02yqqv993","country_code":"RU","type":"education","lineage":["https://openalex.org/I17877952"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"N. I. Zaitseva","raw_affiliation_strings":["The\rFaculty of Pharmacy, First Moscow State Medical University, Moscow 119991, Russia"],"affiliations":[{"raw_affiliation_string":"The\rFaculty of Pharmacy, First Moscow State Medical University, Moscow 119991, Russia","institution_ids":["https://openalex.org/I17877952"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012106039","display_name":"Viacheslav Zosimov","orcid":"https://orcid.org/0000-0003-0824-4168"},"institutions":[{"id":"https://openalex.org/I153845743","display_name":"Moscow Institute of Physics and Technology","ror":"https://ror.org/00v0z9322","country_code":"RU","type":"education","lineage":["https://openalex.org/I153845743"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"V. V. Zosimov","raw_affiliation_strings":["Department\rof Mathematics, Moscow Institute of Physics and Technology, Moscow 117303, Russia"],"affiliations":[{"raw_affiliation_string":"Department\rof Mathematics, Moscow Institute of Physics and Technology, Moscow 117303, Russia","institution_ids":["https://openalex.org/I153845743"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014949338"],"corresponding_institution_ids":["https://openalex.org/I153845743","https://openalex.org/I19880235"],"apc_list":null,"apc_paid":null,"fwci":1.0515,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.80427046,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"55","issue":"10","first_page":"2121","last_page":"2137"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9896000027656555,"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":0.9871000051498413,"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/docking","display_name":"Docking (animal)","score":0.6655024886131287},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49492400884628296},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4462486803531647},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42987269163131714},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3337476849555969},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1765211522579193},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15221697092056274},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08938091993331909}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6655024886131287},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49492400884628296},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4462486803531647},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42987269163131714},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3337476849555969},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1765211522579193},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15221697092056274},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08938091993331909},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"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":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056831","descriptor_name":"Coordination Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056831","descriptor_name":"Coordination Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056831","descriptor_name":"Coordination Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5b00158","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00158","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:26418299","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26418299","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":[{"id":"https://openalex.org/G4235580746","display_name":null,"funder_award_id":"14-14-00598","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1505394602","https://openalex.org/W1516459493","https://openalex.org/W1532848864","https://openalex.org/W1605578858","https://openalex.org/W1969017960","https://openalex.org/W1972148009","https://openalex.org/W1974885083","https://openalex.org/W1977467384","https://openalex.org/W1980253717","https://openalex.org/W1985588649","https://openalex.org/W1987863430","https://openalex.org/W1989971979","https://openalex.org/W1990627326","https://openalex.org/W1993403967","https://openalex.org/W2001956250","https://openalex.org/W2002733813","https://openalex.org/W2003356525","https://openalex.org/W2005817231","https://openalex.org/W2012084558","https://openalex.org/W2013085020","https://openalex.org/W2014417929","https://openalex.org/W2014704001","https://openalex.org/W2014985938","https://openalex.org/W2038542598","https://openalex.org/W2048316372","https://openalex.org/W2050456292","https://openalex.org/W2055410316","https://openalex.org/W2064572456","https://openalex.org/W2066515324","https://openalex.org/W2068468142","https://openalex.org/W2073021822","https://openalex.org/W2073900163","https://openalex.org/W2077467665","https://openalex.org/W2078667512","https://openalex.org/W2084266282","https://openalex.org/W2087621126","https://openalex.org/W2092285329","https://openalex.org/W2100678718","https://openalex.org/W2104533058","https://openalex.org/W2105527266","https://openalex.org/W2107506448","https://openalex.org/W2120898782","https://openalex.org/W2128332459","https://openalex.org/W2132629607","https://openalex.org/W2133773344","https://openalex.org/W2135502915","https://openalex.org/W2148624934","https://openalex.org/W2158360182","https://openalex.org/W2160753576","https://openalex.org/W2169176218","https://openalex.org/W2169678694"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"We":[0,57,177],"analyzed":[1],"the":[2,116,138,146,155,180,183,196,202,208],"frequency":[3],"with":[4,186],"which":[5],"intraligand":[6,39,43,83,190,199],"contacts":[7],"occurred":[8],"in":[9,154],"a":[10,59,65,70,79],"set":[11,50,157],"of":[12,64,72,137,158,182,189,198,205],"1300":[13,159],"protein-ligand":[14,160],"complexes":[15,161],"[":[16,98,119,162],"Plewczynski":[17,163],"et":[18,100,121,164],"al.":[19,101,122,165],"J.":[20,123,166],"Comput.":[21,167],"Chem.":[22,168],"2011":[23,169],",":[24,26,107,109,128,130,170,172],"32":[25,171],"742":[27,173],"-":[28,111,132,174],"755":[29,175],".].":[30,134,176],"Our":[31],"analysis":[32],"showed":[33],"that":[34],"flexible":[35,152],"ligands":[36,153],"often":[37],"form":[38],"hydrophobic":[40],"contacts,":[41],"while":[42],"hydrogen":[44],"bonds":[45,206],"are":[46,195],"rare.":[47],"The":[48,85,135],"test":[49,156],"was":[51,87,141],"also":[52],"thoroughly":[53],"investigated":[54,179],"and":[55,148,201],"classified.":[56],"suggest":[58],"universal":[60],"method":[61,86],"for":[62,82,151],"enhancement":[63,136],"scoring":[66,96,139,149],"function":[67,97,140],"based":[68,114],"on":[69,115],"potential":[71],"mean":[73],"force":[74],"(PMF-based":[75],"score)":[76],"by":[77],"adding":[78],"term":[80],"accounting":[81],"interactions.":[84],"implemented":[88],"via":[89],"in-house":[90],"developed":[91],"program,":[92],"utilizing":[93],"an":[94],"Algo_score":[95],"Ramensky":[99],"Proteins:":[102],"Struct.,":[103],"Funct.,":[104],"Genet.":[105],"2007":[106],"69":[108],"349":[110],"357":[112],".]":[113],"Tarasov-Muryshev":[117],"PMF":[118],"Muryshev":[120],"Comput.-Aided":[124],"Mol.":[125],"Des.":[126],"2003":[127],"17":[129],"597":[131],"605":[133],"shown":[142],"to":[143,212],"significantly":[144],"improve":[145],"docking":[147,184],"quality":[150],"then":[178],"correlation":[181],"results":[185],"two":[187],"parameters":[188,194],"interactions":[191,200],"estimation.":[192],"These":[193],"weight":[197],"minimum":[203],"number":[204],"between":[207],"ligand":[209],"atoms":[210],"required":[211],"take":[213],"their":[214],"interaction":[215],"into":[216],"account.":[217]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
