{"id":"https://openalex.org/W6986728792","doi":null,"title":"Protein Conformational Dynamics In Genomic Analysis","display_name":"Protein Conformational Dynamics In Genomic Analysis","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W6986728792"},"language":"en","primary_location":{"id":"pmh:item:41277","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2286/R.I.41277","pdf_url":"http://hdl.handle.net/2286/R.I.41277","source":{"id":"https://openalex.org/S4306400254","display_name":"Arizona State University Library Digital Repository (Arizona State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I55732556","host_organization_name":"Arizona State University","host_organization_lineage":["https://openalex.org/I55732556"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Doctoral Dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2286/R.I.41277","any_repository_has_fulltext":true},"authorships":[],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"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":true,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9937000274658203,"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":0.9937000274658203,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.004100000020116568,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.0005000000237487257,"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-conformational-dynamics","display_name":"protein conformational dynamics","score":0.984000027179718},{"id":"https://openalex.org/keywords/single-nucleotide-variants","display_name":"single nucleotide variants","score":0.9629999995231628},{"id":"https://openalex.org/keywords/disease-associated-mutations","display_name":"disease-associated mutations","score":0.7239999771118164},{"id":"https://openalex.org/keywords/lysosomal-storage-disorders","display_name":"lysosomal storage disease","score":0.49799999594688416},{"id":"https://openalex.org/keywords/coevolution","display_name":"coevolution","score":0.6050000190734863},{"id":"https://openalex.org/keywords/amino-acid-sequence-conservation","display_name":"amino acid conservation","score":0.6980000138282776},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"protein function prediction","score":0.4440000057220459}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.6972000002861023},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5325999855995178},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.5135999917984009},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5109000205993652},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4887000024318695},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4526999890804291},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.450300008058548},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.44020000100135803},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4268999993801117},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.40880000591278076},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4065000116825104},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.39100000262260437},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.3792000114917755},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.37549999356269836},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3598000109195709},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.34459999203681946},{"id":"https://openalex.org/C109964505","wikidata":"https://www.wikidata.org/wiki/Q3321436","display_name":"Allosteric enzyme","level":4,"score":0.33889999985694885},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.32919999957084656},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.3255999982357025},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.3244999945163727},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.32190001010894775},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.32109999656677246},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.3050000071525574},{"id":"https://openalex.org/C149129301","wikidata":"https://www.wikidata.org/wiki/Q3883802","display_name":"Neutral mutation","level":3,"score":0.29170000553131104},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2825999855995178},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2786000072956085},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.26840001344680786},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.265500009059906},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2648000121116638},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.26420000195503235},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.2581000030040741},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.25760000944137573},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2554999887943268}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:item:41277","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2286/R.I.41277","pdf_url":"http://hdl.handle.net/2286/R.I.41277","source":{"id":"https://openalex.org/S4306400254","display_name":"Arizona State University Library Digital Repository (Arizona State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I55732556","host_organization_name":"Arizona State University","host_organization_lineage":["https://openalex.org/I55732556"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Doctoral Dissertation"}],"best_oa_location":{"id":"pmh:item:41277","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2286/R.I.41277","pdf_url":"http://hdl.handle.net/2286/R.I.41277","source":{"id":"https://openalex.org/S4306400254","display_name":"Arizona State University Library Digital Repository (Arizona State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I55732556","host_organization_name":"Arizona State University","host_organization_lineage":["https://openalex.org/I55732556"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Doctoral Dissertation"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.504800021648407}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W6986728792.pdf","grobid_xml":"https://content.openalex.org/works/W6986728792.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2108267147","https://openalex.org/W2977829233","https://openalex.org/W2013253738","https://openalex.org/W2020802535","https://openalex.org/W2903084665","https://openalex.org/W2792419324","https://openalex.org/W1587767001","https://openalex.org/W3007324177","https://openalex.org/W2801491392","https://openalex.org/W7125202964"],"abstract_inverted_index":{"abstract:":[0],"Proteins":[1],"are":[2,69,120],"essential":[3],"for":[4,178,341],"most":[5,71],"biological":[6],"processes":[7],"that":[8,88,142,168,252,281,320],"constitute":[9],"life.":[10],"The":[11,97],"function":[12,62,107],"of":[13,29,34,74,84,86,104,147,156,159,206,226,236,300,326,337],"a":[14,35,51,130,135,148,227,233,315,327],"protein":[15,55,61,211,328],"is":[16,24,108,151],"encoded":[17],"within":[18],"its":[19,27],"3D":[20,339],"folded":[21],"structure,":[22],"which":[23,57,150,199],"determined":[25],"by":[26,329],"sequence":[28,49],"amino":[30,47,115],"acids.":[31],"A":[32],"variation":[33],"single":[36],"nucleotide":[37],"in":[38,53,76,123,153],"the":[39,46,54,70,102,124,157,172,201,210,213,261,298,323,335,338],"DNA":[40],"during":[41],"transcription":[42],"(nSNV)":[43],"can":[44,58,89,170,292,321],"alter":[45],"acid":[48,116],"(i.e.,":[50,216,264],"mutation":[52],"sequence),":[56],"adversely":[59],"impact":[60,103,158],"and":[63,78,174,232,243],"sometimes":[64],"cause":[65],"disease.":[66,96],"These":[67,118],"mutations":[68,225],"prevalent":[72],"form":[73],"variations":[75],"humans,":[77],"each":[79],"individual":[80],"genome":[81],"harbors":[82],"tens":[83],"thousands":[85],"nSNVs":[87,105,160],"be":[90],"benign":[91],"(neutral)":[92],"or":[93],"lead":[94],"to":[95,100,271,296],"primary":[98],"way":[99],"assess":[101],"on":[106,113,161,209],"through":[109],"evolutionary":[110,183],"approaches":[111,119,184,295],"based":[112,288],"positional":[114],"conservation.":[117],"largely":[121],"inadequate":[122],"regime":[125],"where":[126,182],"positions":[127,181],"evolve":[128],"at":[129],"fast":[131,179],"rate.":[132],"We":[133,188],"developed":[134],"method":[136],"called":[137,230],"dynamic":[138,195,202,256],"flexibility":[139],"index":[140,197],"(DFI)":[141],"measures":[143,200],"site-specific":[144],"conformational":[145,286],"dynamics":[146,287,324],"protein,":[149],"paramount":[152],"exploring":[154],"mechanisms":[155],"function.":[162],"In":[163,247],"this":[164],"thesis,":[165],"we":[166,221,250,313],"demonstrate":[167],"DFI":[169],"distinguish":[171],"disease-associated":[173],"neutral":[175,242],"nSNVs,":[176],"particularly":[177],"evolving":[180],"lack":[185],"predictive":[186],"power.":[187],"also":[189],"describe":[190],"an":[191,268],"additional":[192],"dynamics-based":[193],"metric,":[194],"coupling":[196,205,259],"(DCI),":[198],"allosteric":[203,257],"residue":[204,258],"distal":[207],"sites":[208,253,263],"with":[212,254,260],"functionally":[214],"critical":[215],"active)":[217],"sites.":[218],"Through":[219],"DCI,":[220],"analyzed":[222],"200":[223],"disease":[224,245,273,302,310],"specific":[228],"enzyme":[229],"GCase,":[231],"proteome-wide":[234,278],"analysis":[235,279],"75":[237],"human":[238],"enzymes":[239],"containing":[240],"323":[241],"362":[244],"mutations.":[246],"both":[248],"cases":[249],"observed":[251],"high":[255],"functional":[262],"DARC":[265],"spots)":[266],"have":[267],"increased":[269],"susceptibility":[270],"harboring":[272],"nSNVs.":[274,303],"Overall,":[275],"our":[276],"comprehensive":[277],"suggests":[280],"incorporating":[282],"these":[283],"novel":[284],"position-specific":[285],"metrics":[289],"into":[290],"genomics":[291],"complement":[293],"current":[294],"increase":[297],"accuracy":[299],"diagnosing":[301],"Furthermore,":[304],"they":[305],"provide":[306],"mechanistic":[307],"insights":[308],"about":[309],"development.":[311],"Lastly,":[312],"introduce":[314],"new,":[316],"purely":[317],"sequence-based":[318],"model":[319],"estimate":[322],"profile":[325],"only":[330],"utilizing":[331],"coevolution":[332],"information,":[333],"eliminating":[334],"requirement":[336],"structure":[340],"determining":[342],"dynamics.":[343]},"counts_by_year":[],"updated_date":"2026-08-30T07:30:35.949966","created_date":"2025-10-10T00:00:00"}