{"id":"https://openalex.org/W2900582736","doi":null,"title":"Optimization and machine learning methods for Computational Protein Docking","display_name":"Optimization and machine learning methods for Computational Protein Docking","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2900582736","mag":"2900582736"},"language":"en","primary_location":{"id":"pmh:oai:open.bu.edu:2144/32673","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/2144/32673","pdf_url":null,"source":{"id":"https://openalex.org/S4306402384","display_name":"OpenBU (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis/Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"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/A5054703399","display_name":"Shahrooz Zarbafian","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shahrooz Zarbafian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5054703399"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.98580002784729,"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":0.98580002784729,"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":0.007400000002235174,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.002199999988079071,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/rigid-transformation","display_name":"rigid transformation","score":0.37599998712539673},{"id":"https://openalex.org/keywords/riemannian-metrics","display_name":"Riemannian metrics","score":0.8109999895095825},{"id":"https://openalex.org/keywords/rmsd","display_name":"RMSD","score":0.546999990940094},{"id":"https://openalex.org/keywords/local-optimization","display_name":"local optimization","score":0.5529999732971191},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"dimensionality reduction","score":0.7429999709129333},{"id":"https://openalex.org/keywords/protein-protein-interaction-prediction","display_name":"protein-protein interaction prediction","score":0.7260000109672546},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.7459999918937683},{"id":"https://openalex.org/keywords/protein-protein-docking","display_name":"protein-protein docking","score":0.4410000145435333},{"id":"https://openalex.org/keywords/scoring-functions","display_name":"scoring functions","score":0.4269999861717224},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"drug discovery","score":0.5139999985694885}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7586192488670349},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.5902785658836365},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5785934925079346},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49597296118736267},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4563407003879547},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.1026594340801239},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.09408864378929138},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09068754315376282},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.08083480596542358},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0647401213645935},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:open.bu.edu:2144/32673","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/2144/32673","pdf_url":null,"source":{"id":"https://openalex.org/S4306402384","display_name":"OpenBU (Boston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I111088046","host_organization_name":"Boston University","host_organization_lineage":["https://openalex.org/I111088046"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis/Dissertation"},{"id":"mag:2900582736","doi":null,"is_oa":false,"landing_page_url":"https://open.bu.edu/handle/2144/32673","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W41908379","https://openalex.org/W255996521","https://openalex.org/W289820477","https://openalex.org/W1030883578","https://openalex.org/W1500036797","https://openalex.org/W1564897360","https://openalex.org/W1600604896","https://openalex.org/W1673310716","https://openalex.org/W1884347414","https://openalex.org/W1899503782","https://openalex.org/W1969554454","https://openalex.org/W1973974137","https://openalex.org/W1976937534","https://openalex.org/W1979670056","https://openalex.org/W1983304433","https://openalex.org/W1985588649","https://openalex.org/W1992806534","https://openalex.org/W1993951624","https://openalex.org/W1996078098","https://openalex.org/W1997084106","https://openalex.org/W1999613943","https://openalex.org/W2000383223","https://openalex.org/W2008706351","https://openalex.org/W2011658408","https://openalex.org/W2021041804","https://openalex.org/W2032392220","https://openalex.org/W2035282876","https://openalex.org/W2036835637","https://openalex.org/W2037412278","https://openalex.org/W2042965115","https://openalex.org/W2050159278","https://openalex.org/W2052789270","https://openalex.org/W2056132907","https://openalex.org/W2065101872","https://openalex.org/W2067455153","https://openalex.org/W2092360980","https://openalex.org/W2094280270","https://openalex.org/W2098740506","https://openalex.org/W2110057983","https://openalex.org/W2111387452","https://openalex.org/W2113030357","https://openalex.org/W2113307443","https://openalex.org/W2115570685","https://openalex.org/W2119555549","https://openalex.org/W2127594538","https://openalex.org/W2129454543","https://openalex.org/W2130479394","https://openalex.org/W2134056721","https://openalex.org/W2134059200","https://openalex.org/W2137219016","https://openalex.org/W2143099339","https://openalex.org/W2145154167","https://openalex.org/W2150399099","https://openalex.org/W2153768000","https://openalex.org/W2159026209","https://openalex.org/W2162166182","https://openalex.org/W2165890129","https://openalex.org/W2171249995","https://openalex.org/W2171755502","https://openalex.org/W2255400221","https://openalex.org/W2560410107","https://openalex.org/W2572080171","https://openalex.org/W2578119541","https://openalex.org/W2588962857","https://openalex.org/W2771169143","https://openalex.org/W2911964244","https://openalex.org/W2915344963","https://openalex.org/W3120231655","https://openalex.org/W4292402580"],"related_works":["https://openalex.org/W2057445270","https://openalex.org/W2407125554","https://openalex.org/W2797906773","https://openalex.org/W2094801760","https://openalex.org/W2303847839","https://openalex.org/W7095129938","https://openalex.org/W2778809918","https://openalex.org/W7097086124","https://openalex.org/W2789371235","https://openalex.org/W1980183605"],"abstract_inverted_index":{"Computational":[0],"Protein":[1,212,366],"Docking":[2],"(CPD)":[3],"is":[4,26,140,147,163,194,197,215,235,263,267,285,345,387,411,435,495],"defined":[5],"as":[6,29,165,187,229],"determining":[7],"the":[8,34,38,45,56,79,125,131,137,168,174,182,201,218,250,272,275,283,295,311,323,336,393,402,409,442,445,455,466,473,483,487],"stable":[9],"complex":[10],"of":[11,75,92,121,128,133,144,170,173,181,184,233,260,279,290,330,335,342,351,388,408,430,444,462,485],"docked":[12],"proteins":[13],"given":[14,380],"information":[15],"about":[16],"two":[17,362],"individual":[18],"partners,":[19],"called":[20],"receptor":[21,381],"and":[22,68,116,155,223,239,258,282,305,326,328,382,420,478,482],"ligand.":[23,175],"The":[24,59,142,161,237,265,298,333,406,437],"problem":[25,81,132,162,475],"often":[27],"formulated":[28,164],"an":[30,398],"energy/score":[31],"minimization":[32],"where":[33,271],"decision":[35],"variables":[36,43,51,225],"are":[37,65,246,277,476],"6":[39],"rigid":[40,171,185],"body":[41],"transformation":[42],"for":[44,241,256,360,391,416,427,490],"ligand":[46,261,280,383],"in":[47,55,63,136,211,365,374,401,480],"addition":[48],"to":[49,53,101,148,200,274,286,294,376,449,465,472],"more":[50,112,119,157],"corresponding":[52],"flexibilities":[54],"protein":[57,153,343,395,432],"structures.":[58],"scoring":[60,99,114,324],"functions":[61,115],"used":[62,210],"CPD":[64],"highly":[66],"nonlinear":[67],"nonconvex":[69],"with":[70,454],"a":[71,89,97,108,177,188,190,253,268,302,339,370,379,414,431,451,491],"very":[72],"large":[73],"number":[74],"local":[76,134,145,231,243],"minima,":[77],"making":[78],"optimization":[80,135,146,166,244],"particularly":[82],"challenging.":[83],"Consequently,":[84],"most":[85],"docking":[86,433,446,493],"procedures":[87],"employ":[88],"multistage":[90],"strategy":[91],"(i)":[93,368],"Global":[94],"Sampling":[95],"using":[96,111,317,356,486],"coarse":[98],"function":[100,325],"identify":[102],"promising":[103],"areas":[104],"followed":[105],"by":[106],"(ii)":[107,423],"Refinement":[109],"stage":[110,139],"accurate":[113],"possibly":[117],"allowing":[118],"degrees":[120],"freedom.":[122],"\\n":[123,248,347],"\\nIn":[124,249],"first":[126],"part":[127,350],"this":[129,352],"work,":[130],"refinement":[138,259,269,329],"addressed.":[141],"goal":[143,284],"remove":[149],"steric":[150],"clashes":[151],"between":[152,418],"partners":[154],"obtain":[156],"realistic":[158],"score":[159],"values.":[160],"on":[167,226,338,355,413],"space":[169,183],"motions":[172,186],"Employing":[176],"recently":[178],"introduced":[179,195],"representation":[180],"manifold,":[189],"new":[191,219,254,288,308,331],"Riemannian":[192],"metric":[193,220],"that":[196,217],"closely":[198],"related":[199],"Root":[202],"Mean":[203],"Square":[204],"Deviation":[205],"(RMSD)":[206],"distance":[207],"measure":[208],"widely":[209],"Docking.":[213],"It":[214],"argued":[216],"puts":[221],"rotational":[222],"translational":[224],"equal":[227],"footing":[228],"far":[230],"changes":[232],"RMSD":[234],"concerned.":[236],"implications":[238,484],"modifications":[240],"gradient-based":[242],"algorithms":[245],"discussed.":[247,496],"second":[251],"part,":[252],"methodology":[255],"resampling":[257,327],"conformations":[262,281],"introduced.":[264],"algorithm":[266,276,299,337,410],"method":[270],"inputs":[273],"ensembles":[278,289],"generate":[287],"refined":[291],"conformations,":[292,313],"closer":[293],"native":[296,467],"complex.":[297],"builds":[300],"upon":[301],"previous":[303],"work":[304,353],"introduces":[306],"multiple":[307],"innovations:":[309],"Clustering":[310],"input":[312],"performing":[314],"dimensionality":[315],"reduction":[316],"Principle":[318],"Component":[319],"Analysis":[320],"(PCA),":[321],"underestimating":[322],"conformations.":[332],"performance":[334],"comprehensive":[340],"benchmark":[341,415],"complexes":[344],"reported.":[346],"\\nThe":[348],"third":[349],"focuses":[354],"machine":[357,371,438],"learning":[358,372,439],"framework":[359],"addressing":[361],"specific":[363],"problems":[364],"Docking:":[367],"Constructing":[369],"model":[373,440],"order":[375],"predict":[377],"whether":[378],"pair":[384],"interact.":[385],"This":[386],"significant":[389],"importance":[390],"constructing":[392],"so-called":[394],"interaction":[396],"networks,":[397],"critical":[399],"step":[400],"Drug":[403],"Discovery":[404],"process.":[405],"success":[407],"verified":[412],"discrimination":[417],"Biological":[419],"Crystallographic":[421],"Dimers.":[422],"A":[424],"ranking":[425,474],"scheme":[426],"output":[428],"predictions":[429,448,458],"server":[434,447,494],"devised.":[436],"employs":[441],"features":[443],"produce":[450],"ranked":[452,457],"list":[453],"top":[456],"having":[459],"higher":[460],"probability":[461],"being":[463],"close":[464],"solution.":[468],"Two":[469],"state-of-the-art":[470],"approaches":[471],"presented":[477],"compared":[479],"detail":[481],"superior":[488],"approach":[489],"structural":[492]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2018-11-29T00:00:00"}
