{"id":"https://openalex.org/W2576623455","doi":"https://doi.org/10.1155/2017/7167691","title":"Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7","display_name":"Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7","publication_year":2017,"publication_date":"2017-01-16","ids":{"openalex":"https://openalex.org/W2576623455","doi":"https://doi.org/10.1155/2017/7167691","mag":"2576623455","pmid":"https://pubmed.ncbi.nlm.nih.gov/28191015"},"language":"en","primary_location":{"id":"doi:10.1155/2017/7167691","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2017/7167691","pdf_url":"http://downloads.hindawi.com/journals/abi/2017/7167691.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"http://downloads.hindawi.com/journals/abi/2017/7167691.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101695175","display_name":"\u0410.\u0412. \u0421\u0443\u043b\u0438\u043c\u043e\u0432","orcid":"https://orcid.org/0000-0002-8767-642X"},"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. V. Sulimov","raw_affiliation_strings":["Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia"],"raw_orcid":"https://orcid.org/0000-0002-8767-642X","affiliations":[{"raw_affiliation_string":"Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081004260","display_name":"Danil Kutov","orcid":"https://orcid.org/0000-0002-4777-6522"},"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":"D. C. Kutov","raw_affiliation_strings":["Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021128272","display_name":"E. V. Katkova","orcid":"https://orcid.org/0000-0001-9961-4069"},"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":true,"raw_author_name":"E. V. Katkova","raw_affiliation_strings":["Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia"],"raw_orcid":"https://orcid.org/0000-0001-9961-4069","affiliations":[{"raw_affiliation_string":"Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080885688","display_name":"\u0412. \u0411. \u0421\u0443\u043b\u0438\u043c\u043e\u0432","orcid":"https://orcid.org/0000-0002-7102-6107"},"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":"V. B. Sulimov","raw_affiliation_strings":["Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021128272"],"corresponding_institution_ids":["https://openalex.org/I19880235"],"apc_list":null,"apc_paid":null,"fwci":2.7366,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.91059854,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"2017","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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/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/T11162","display_name":"Enzyme Structure and Function","score":0.9994000196456909,"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/maxima-and-minima","display_name":"Maxima and minima","score":0.8105452060699463},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.7613615989685059},{"id":"https://openalex.org/keywords/quantum-chemical","display_name":"Quantum chemical","score":0.7100896835327148},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6815442442893982},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.5177285075187683},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.508683979511261},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4937978684902191},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.465597003698349},{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.43796786665916443},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41509056091308594},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.33150577545166016},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.26902058720588684},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.251999169588089},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.20211908221244812},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1814696490764618},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1734025776386261},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.080670565366745},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07357478141784668}],"concepts":[{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.8105452060699463},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.7613615989685059},{"id":"https://openalex.org/C2991951333","wikidata":"https://www.wikidata.org/wiki/Q188403","display_name":"Quantum chemical","level":3,"score":0.7100896835327148},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6815442442893982},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.5177285075187683},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.508683979511261},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4937978684902191},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.465597003698349},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.43796786665916443},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41509056091308594},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.33150577545166016},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.26902058720588684},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.251999169588089},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.20211908221244812},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1814696490764618},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1734025776386261},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.080670565366745},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07357478141784668},{"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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1155/2017/7167691","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2017/7167691","pdf_url":"http://downloads.hindawi.com/journals/abi/2017/7167691.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28191015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28191015","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":"Advances in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5278191","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5278191","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Adv Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1155/2017/7167691","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2017/7167691","pdf_url":"http://downloads.hindawi.com/journals/abi/2017/7167691.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8600000143051147}],"awards":[{"id":"https://openalex.org/G4061520212","display_name":null,"funder_award_id":"15-11-00025","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":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2576623455.pdf","grobid_xml":"https://content.openalex.org/works/W2576623455.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1492893078","https://openalex.org/W1971803965","https://openalex.org/W1977175169","https://openalex.org/W1985601402","https://openalex.org/W1988636074","https://openalex.org/W1995818918","https://openalex.org/W1996164871","https://openalex.org/W2008558900","https://openalex.org/W2011805684","https://openalex.org/W2025178360","https://openalex.org/W2032084435","https://openalex.org/W2066037747","https://openalex.org/W2078786624","https://openalex.org/W2086126241","https://openalex.org/W2088162897","https://openalex.org/W2111278964","https://openalex.org/W2130479394","https://openalex.org/W2140886907","https://openalex.org/W2147421370","https://openalex.org/W2169307138","https://openalex.org/W2205473393","https://openalex.org/W2285349883","https://openalex.org/W2317090635","https://openalex.org/W2323519269","https://openalex.org/W2331194795","https://openalex.org/W2333083696","https://openalex.org/W2403926370","https://openalex.org/W2530722635"],"related_works":["https://openalex.org/W4284966708","https://openalex.org/W2041791898","https://openalex.org/W2152236566","https://openalex.org/W3212787082","https://openalex.org/W2030423316","https://openalex.org/W3135856311","https://openalex.org/W2573149326","https://openalex.org/W2005817231","https://openalex.org/W3195854494","https://openalex.org/W1997409847"],"abstract_inverted_index":{"Results":[0],"of":[1,5,25,81,140],"the":[2,6,11,22,33,40,45,54,67,87,117,124,128,133,141],"combined":[3],"use":[4],"classical":[7],"force":[8,47],"field":[9,48],"and":[10,78,105],"recent":[12,88],"quantum":[13,89],"chemical":[14,90],"PM7":[15,92],"method":[16],"for":[17],"docking":[18,24,68],"are":[19,64,76,84],"presented.":[20],"Initially":[21],"gridless":[23],"a":[26],"flexible":[27],"low":[28],"molecular":[29],"weight":[30],"ligand":[31,125,130,142],"into":[32],"rigid":[34],"target":[35],"protein":[36],"is":[37,96,150],"performed":[38],"with":[39,49,86,102,146],"energy":[41,74,113,119,148],"function":[42],"calculated":[43],"in":[44,53,66,116,132],"MMFF94":[46,147],"implicit":[50],"water":[51],"solvent":[52],"PCM":[55],"model.":[56],"Among":[57],"several":[58],"hundred":[59],"thousand":[60,72],"local":[61],"minima,":[62],"which":[63],"found":[65],"procedure,":[69],"about":[70],"eight":[71],"lowest":[73],"minima":[75,83],"chosen":[77],"then":[79],"energies":[80],"these":[82],"recalculated":[85],"semiempirical":[91],"method.":[93],"This":[94],"procedure":[95],"applied":[97],"to":[98,123],"16":[99],"test":[100,110],"complexes":[101,111],"different":[103],"proteins":[104],"ligands.":[106],"For":[107],"almost":[108],"all":[109],"such":[112],"recalculation":[114],"results":[115],"global":[118],"minimum":[120],"configuration":[121],"corresponding":[122],"pose":[126],"near":[127],"native":[129],"position":[131],"crystalized":[134],"protein-ligand":[135],"complex.":[136],"A":[137],"significant":[138],"improvement":[139],"positioning":[143],"accuracy":[144],"comparing":[145],"calculations":[149],"demonstrated.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}