{"id":"https://openalex.org/W63336964","doi":null,"title":"Large-Scale Analysis of Protein-Ligand Binding Sites using the Binding MOAD Database.","display_name":"Large-Scale Analysis of Protein-Ligand Binding Sites using the Binding MOAD Database.","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W63336964","mag":"63336964"},"language":"en","primary_location":{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/91400","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/91400","pdf_url":"https://hdl.handle.net/2027.42/91400","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/2027.42/91400","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011957277","display_name":"Nickolay A. Khazanov","orcid":"https://orcid.org/0000-0003-0368-7824","observed_orcids":["https://orcid.org/0000-0003-0368-7824"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Nickolay A. Khazanov","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-0368-7824","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5011957277"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9883000254631042,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9883000254631042,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.006300000008195639,"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/T11162","display_name":"Enzyme Structure and Function","score":0.002099999925121665,"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/protein-ligand-binding-sites","display_name":"protein-ligand binding sites","score":0.9879999756813049},{"id":"https://openalex.org/keywords/binding-site-prediction","display_name":"binding site prediction","score":0.8330000042915344},{"id":"https://openalex.org/keywords/structure-based-drug-design","display_name":"structure-based drug design","score":0.847000002861023},{"id":"https://openalex.org/keywords/computational-proteomics","display_name":"computational proteomics","score":0.6320000290870667},{"id":"https://openalex.org/keywords/protein-ligand-complex","display_name":"protein-ligand complex","score":0.765999972820282}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4407997727394104},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4342087209224701},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3888677656650543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.374085932970047},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3321593403816223},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3271714150905609},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32376667857170105},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.24644550681114197},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24234536290168762},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.13607540726661682}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/91400","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/91400","pdf_url":"https://hdl.handle.net/2027.42/91400","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:63336964","doi":null,"is_oa":false,"landing_page_url":"https://deepblue.lib.umich.edu/handle/2027.42/91400","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":{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/91400","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/91400","pdf_url":"https://hdl.handle.net/2027.42/91400","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G8801575875","display_name":"CAREER: Protein-Ligand Databases in the Lab and Classroom","funder_award_id":"0546073","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W63336964.pdf","grobid_xml":"https://content.openalex.org/works/W63336964.grobid-xml"},"referenced_works_count":213,"referenced_works":["https://openalex.org/W36632936","https://openalex.org/W255996521","https://openalex.org/W1505394602","https://openalex.org/W1517566065","https://openalex.org/W1518416799","https://openalex.org/W1530397352","https://openalex.org/W1543932334","https://openalex.org/W1585634379","https://openalex.org/W1592950931","https://openalex.org/W1597533137","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1840257347","https://openalex.org/W1939083266","https://openalex.org/W1964640688","https://openalex.org/W1965207004","https://openalex.org/W1967005434","https://openalex.org/W1967809254","https://openalex.org/W1969370763","https://openalex.org/W1969774361","https://openalex.org/W1969888071","https://openalex.org/W1971618381","https://openalex.org/W1971700621","https://openalex.org/W1972148009","https://openalex.org/W1973098530","https://openalex.org/W1973816625","https://openalex.org/W1974499817","https://openalex.org/W1974638435","https://openalex.org/W1974732853","https://openalex.org/W1979147581","https://openalex.org/W1979414133","https://openalex.org/W1979598348","https://openalex.org/W1980285986","https://openalex.org/W1981385422","https://openalex.org/W1981625739","https://openalex.org/W1983803895","https://openalex.org/W1984100064","https://openalex.org/W1984197379","https://openalex.org/W1985028250","https://openalex.org/W1986154009","https://openalex.org/W1987150763","https://openalex.org/W1987688066","https://openalex.org/W1988111902","https://openalex.org/W1988640094","https://openalex.org/W1990355168","https://openalex.org/W1990598130","https://openalex.org/W1993046136","https://openalex.org/W1993976538","https://openalex.org/W1994250273","https://openalex.org/W1996423252","https://openalex.org/W1999319994","https://openalex.org/W2001415793","https://openalex.org/W2001900040","https://openalex.org/W2002827932","https://openalex.org/W2003356525","https://openalex.org/W2003806043","https://openalex.org/W2004178884","https://openalex.org/W2004360551","https://openalex.org/W2004837736","https://openalex.org/W2005153862","https://openalex.org/W2006197769","https://openalex.org/W2008517160","https://openalex.org/W2009297402","https://openalex.org/W2012084558","https://openalex.org/W2018056833","https://openalex.org/W2019951137","https://openalex.org/W2021954541","https://openalex.org/W2022058405","https://openalex.org/W2023790301","https://openalex.org/W2024463335","https://openalex.org/W2025043912","https://openalex.org/W2025458374","https://openalex.org/W2028083131","https://openalex.org/W2029582401","https://openalex.org/W2030495049","https://openalex.org/W2030517878","https://openalex.org/W2030589493","https://openalex.org/W2030729456","https://openalex.org/W2031194866","https://openalex.org/W2032675576","https://openalex.org/W2035292911","https://openalex.org/W2040219737","https://openalex.org/W2043199972","https://openalex.org/W2043886357","https://openalex.org/W2047229337","https://openalex.org/W2049334204","https://openalex.org/W2050456292","https://openalex.org/W2051594610","https://openalex.org/W2051993924","https://openalex.org/W2052030759","https://openalex.org/W2058463742","https://openalex.org/W2059536443","https://openalex.org/W2060468500","https://openalex.org/W2060495448","https://openalex.org/W2061079400","https://openalex.org/W2063831812","https://openalex.org/W2067732724","https://openalex.org/W2067865468","https://openalex.org/W2068265376","https://openalex.org/W2072180710","https://openalex.org/W2072287929","https://openalex.org/W2072682248","https://openalex.org/W2076127975","https://openalex.org/W2076779488","https://openalex.org/W2079672600","https://openalex.org/W2079953901","https://openalex.org/W2080653934","https://openalex.org/W2081201773","https://openalex.org/W2082388363","https://openalex.org/W2085142174","https://openalex.org/W2087254300","https://openalex.org/W2088534163","https://openalex.org/W2090280616","https://openalex.org/W2090640471","https://openalex.org/W2091326717","https://openalex.org/W2091563009","https://openalex.org/W2091734240","https://openalex.org/W2092234666","https://openalex.org/W2092285329","https://openalex.org/W2093347105","https://openalex.org/W2094118945","https://openalex.org/W2094148990","https://openalex.org/W2094696459","https://openalex.org/W2096864392","https://openalex.org/W2097233276","https://openalex.org/W2097642323","https://openalex.org/W2097856882","https://openalex.org/W2098312592","https://openalex.org/W2100494857","https://openalex.org/W2100986312","https://openalex.org/W2101220662","https://openalex.org/W2102475449","https://openalex.org/W2102794349","https://openalex.org/W2103794058","https://openalex.org/W2105527266","https://openalex.org/W2105869636","https://openalex.org/W2105902442","https://openalex.org/W2107103206","https://openalex.org/W2108138353","https://openalex.org/W2109539263","https://openalex.org/W2110562802","https://openalex.org/W2112109058","https://openalex.org/W2112794559","https://openalex.org/W2112878061","https://openalex.org/W2114779636","https://openalex.org/W2115312817","https://openalex.org/W2115336138","https://openalex.org/W2115592403","https://openalex.org/W2115713787","https://openalex.org/W2116099439","https://openalex.org/W2117385703","https://openalex.org/W2118233996","https://openalex.org/W2121481607","https://openalex.org/W2121895929","https://openalex.org/W2122199548","https://openalex.org/W2123373099","https://openalex.org/W2125106761","https://openalex.org/W2125200271","https://openalex.org/W2127059639","https://openalex.org/W2127648442","https://openalex.org/W2127866370","https://openalex.org/W2128332459","https://openalex.org/W2128402268","https://openalex.org/W2130027818","https://openalex.org/W2130393164","https://openalex.org/W2130479394","https://openalex.org/W2132122858","https://openalex.org/W2132629607","https://openalex.org/W2133657429","https://openalex.org/W2133990057","https://openalex.org/W2134326554","https://openalex.org/W2135502915","https://openalex.org/W2135910194","https://openalex.org/W2136567909","https://openalex.org/W2137146016","https://openalex.org/W2137841449","https://openalex.org/W2137991504","https://openalex.org/W2138473864","https://openalex.org/W2138512826","https://openalex.org/W2138770756","https://openalex.org/W2140407975","https://openalex.org/W2142338805","https://openalex.org/W2143567718","https://openalex.org/W2144258433","https://openalex.org/W2144714500","https://openalex.org/W2144998676","https://openalex.org/W2145682943","https://openalex.org/W2146465875","https://openalex.org/W2147691086","https://openalex.org/W2152326664","https://openalex.org/W2153341679","https://openalex.org/W2154709258","https://openalex.org/W2155275960","https://openalex.org/W2155744824","https://openalex.org/W2156207120","https://openalex.org/W2158534713","https://openalex.org/W2158630348","https://openalex.org/W2158714788","https://openalex.org/W2162166182","https://openalex.org/W2163169974","https://openalex.org/W2163352757","https://openalex.org/W2164088236","https://openalex.org/W2165526004","https://openalex.org/W2167857557","https://openalex.org/W2169064131","https://openalex.org/W2169562071","https://openalex.org/W2171234651","https://openalex.org/W2217901364","https://openalex.org/W2414367973","https://openalex.org/W2430084315","https://openalex.org/W2949504121","https://openalex.org/W4230141118","https://openalex.org/W4235295213"],"related_works":["https://openalex.org/W2060886672","https://openalex.org/W2137841449","https://openalex.org/W2146465875","https://openalex.org/W6999404959","https://openalex.org/W2217901364","https://openalex.org/W2908828763","https://openalex.org/W6940173565","https://openalex.org/W2168580221","https://openalex.org/W4416907357","https://openalex.org/W1994250273"],"abstract_inverted_index":{"Current":[0],"structure-based":[1],"drug":[2],"design":[3],"(SBDD)":[4],"methods":[5,25,343],"require":[6],"understanding":[7],"of":[8,11,16,48,60,70,85,109,118,124,130,141,153,176,278,296,314,329,338],"general":[9,43],"tends":[10],"protein-ligand":[12,49,63,211,330],"interactions.":[13],"Informative":[14],"descriptors":[15,34],"ligand-binding":[17,113],"sites":[18,87,123,265],"provide":[19,146],"powerful":[20],"heuristics":[21],"to":[22,27,65,75,81,97,128,145,172,186,189,222,236,258,318,333,341],"improve":[23,173,205],"SBDD":[24],"designed":[26],"infer":[28],"function":[29],"from":[30,227],"protein":[31],"structure.":[32],"These":[33],"must":[35],"have":[36],"a":[37,104,177,217,251,286,307],"solid":[38],"statistical":[39],"foundation":[40],"for":[41,106,121,148,261,275,344],"assessing":[42],"trends":[44,117,143],"in":[45,161,193,232,240],"large":[46,199],"sets":[47],"complexes.":[50],"This":[51,92],"dissertation":[52,316],"focuses":[53],"on":[54,158,302],"mining":[55],"the":[56,95,116,139,151,154,159,174,190,206,220,241,315,325,335],"Binding":[57,76],"MOAD":[58],"database":[59],"highly":[61],"curated":[62],"complexes":[64,331],"determine":[66,138],"frequently":[67],"observed":[68],"patterns":[69],"binding-site":[71,167,179,321],"composition.":[72],"An":[73],"extension":[74],"MOAD\u2019s":[77],"framework":[78,96],"is":[79,164],"developed":[80],"store":[82],"structural":[83,287,304],"details":[84],"binding":[86,122],"and":[88,144,202,269,332],"facilitate":[89],"large-scale":[90],"analysis.":[91],"thesis":[93],"uses":[94],"address":[98],"three":[99],"topics.":[100],"It":[101],"first":[102],"describes":[103,285],"strategy":[105],"determining":[107],"over-representation":[108],"amino":[110],"acids":[111],"within":[112,324],"sites,":[114],"comparing":[115],"residue":[119,168],"propensity":[120,162],"biologically":[125,224,263],"relevant":[126,225,264],"ligands":[127,226,279],"those":[129],"spurious":[131,267],"molecules":[132,230],"with":[133],"no":[134],"known":[135],"function.":[136],"To":[137],"significance":[140],"these":[142],"guidelines":[147],"residue-propensity":[149],"studies,":[150],"effect":[152],"data":[155,323,340],"set":[156,328],"size":[157],"variation":[160],"values":[163],"evaluated.":[165],"Next,":[166],"propensities":[169],"are":[170,184,214,248,256,317],"applied":[171],"performance":[175],"geometry-based,":[178],"prediction":[180],"algorithm.":[181],"Propensity-based":[182],"scores":[183,204],"found":[185,257],"perform":[187,259],"comparably":[188],"native":[191],"score":[192],"successfully":[194],"ranking":[195,262],"correct":[196],"predictions.":[197],"For":[198],"proteins,":[200],"propensity-based":[201],"consensus":[203],"scoring":[207,212,246],"success.":[208],"Finally,":[209],"current":[210],"functions":[213,247],"evaluated":[215,249],"using":[216,306],"new":[218],"criterion:":[219],"ability":[221],"discern":[223],"\u201copportunistic":[228],"binders,\u201d":[229],"present":[231],"crystal":[233],"structures":[234],"due":[235],"their":[237,303],"high":[238],"concentrations":[239],"crystallization":[242],"medium.":[243],"Four":[244],"different":[245],"against":[250],"diverse":[252],"benchmark":[253],"set.":[254],"All":[255],"well":[260],"over":[266],"ones,":[268],"all":[270],"performed":[271],"best":[272],"when":[273],"penalties":[274],"torsional":[276],"strain":[277],"were":[280],"included.":[281],"The":[282,311],"final":[283],"chapter":[284],"alignment":[288],"method,":[289],"termed":[290],"HwRMSD,":[291],"which":[292],"can":[293],"align":[294],"proteins":[295],"very":[297],"low":[298],"sequence":[299],"homology":[300],"based":[301],"similarity":[305],"weighted":[308],"structure":[309],"superposition.":[310],"overall":[312],"aims":[313],"collect":[319],"high-quality":[320],"composition":[322],"largest":[326],"available":[327],"evaluate":[334],"appropriate":[336],"applications":[337],"this":[339],"emerging":[342],"computational":[345],"proteomics.":[346]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
