{"id":"https://openalex.org/W7171537466","doi":"https://doi.org/10.1145/3807503.3819504","title":"Context-based Hierarchical Backbone-Dependent Rotamer Library","display_name":"Context-based Hierarchical Backbone-Dependent Rotamer Library","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171537466","doi":"https://doi.org/10.1145/3807503.3819504"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819504","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819504","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819504","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005997198","display_name":"Kamal Al Nasr","orcid":"https://orcid.org/0000-0001-8459-9070"},"institutions":[{"id":"https://openalex.org/I75256744","display_name":"Tennessee State University","ror":"https://ror.org/01fpczx89","country_code":"US","type":"education","lineage":["https://openalex.org/I75256744"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kamal Al Nasr","raw_affiliation_strings":["Tennessee state university, Nashville, USA"],"raw_orcid":"https://orcid.org/0000-0001-8459-9070","affiliations":[{"raw_affiliation_string":"Tennessee state university, Nashville, USA","institution_ids":["https://openalex.org/I75256744"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120203846","display_name":"Ahmad Jad Allah","orcid":"https://orcid.org/0009-0002-3301-0371"},"institutions":[{"id":"https://openalex.org/I75256744","display_name":"Tennessee State University","ror":"https://ror.org/01fpczx89","country_code":"US","type":"education","lineage":["https://openalex.org/I75256744"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ahmad Jad Allah","raw_affiliation_strings":["Tennessee state university, Nashville, USA"],"raw_orcid":"https://orcid.org/0009-0002-3301-0371","affiliations":[{"raw_affiliation_string":"Tennessee state university, Nashville, USA","institution_ids":["https://openalex.org/I75256744"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104347592","display_name":"Mohammed Alamri","orcid":"https://orcid.org/0009-0002-5459-0766"},"institutions":[{"id":"https://openalex.org/I75256744","display_name":"Tennessee State University","ror":"https://ror.org/01fpczx89","country_code":"US","type":"education","lineage":["https://openalex.org/I75256744"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammad Alamri","raw_affiliation_strings":["Tennessee state university, Nashville, USA"],"raw_orcid":"https://orcid.org/0009-0002-5459-0766","affiliations":[{"raw_affiliation_string":"Tennessee state university, Nashville, USA","institution_ids":["https://openalex.org/I75256744"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037256841","display_name":"Mohammad Al Sallal","orcid":"https://orcid.org/0000-0002-4409-9562"},"institutions":[{"id":"https://openalex.org/I75256744","display_name":"Tennessee State University","ror":"https://ror.org/01fpczx89","country_code":"US","type":"education","lineage":["https://openalex.org/I75256744"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammad Al Sallal","raw_affiliation_strings":["Tennessee state university, Nashville, USA"],"raw_orcid":"https://orcid.org/0000-0002-4409-9562","affiliations":[{"raw_affiliation_string":"Tennessee state university, Nashville, USA","institution_ids":["https://openalex.org/I75256744"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I75256744"],"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":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.3253999948501587},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.25839999318122864},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.25609999895095825},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.24250000715255737},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.23559999465942383}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.517799973487854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39309999346733093},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3253999948501587},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2856999933719635},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.26759999990463257},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.25839999318122864},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.24250000715255737},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.23559999465942383},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2345999926328659}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819504","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819504","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819504","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819504","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1574312817","https://openalex.org/W1992426410","https://openalex.org/W2011658408","https://openalex.org/W2027189612","https://openalex.org/W2039388179","https://openalex.org/W2049659492","https://openalex.org/W2065283382","https://openalex.org/W2092387745","https://openalex.org/W2106648157","https://openalex.org/W2112489703","https://openalex.org/W2129305902","https://openalex.org/W2150155770","https://openalex.org/W2153153865","https://openalex.org/W2164130591","https://openalex.org/W2201713963","https://openalex.org/W2324653063","https://openalex.org/W2891623559","https://openalex.org/W3020957661","https://openalex.org/W4306721750","https://openalex.org/W4378782828","https://openalex.org/W4384119675","https://openalex.org/W4395053034","https://openalex.org/W4415735116","https://openalex.org/W7140123830"],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"modeling":[1],"of":[2,116,136,156],"sidechain":[3,28],"conformations":[4],"is":[5],"essential":[6],"for":[7,41,166],"protein":[8],"structure":[9,110,179],"prediction":[10],"and":[11,27,46,69,72,85,119,131],"design.":[12],"Backbone-dependent":[13],"rotamer":[14,57,78],"libraries":[15,32],"have":[16],"been":[17],"highly":[18],"successful":[19],"in":[20],"revealing":[21],"the":[22,62,125,137,143,145,157,175,182],"relation":[23],"between":[24],"backbone":[25,36,139],"geometry":[26],"preferences.":[29],"However,":[30],"these":[31],"depend":[33],"excessively":[34],"on":[35,127],"torsions":[37],"which":[38],"limit":[39],"accuracy":[40,149],"residues":[42,167],"with":[43,97,168],"flexible":[44],"sidechains":[45],"context-dependent":[47],"interactions.":[48],"In":[49,75,142],"this":[50,76],"research,":[51],"we":[52],"propose":[53],"a":[54],"hierarchical,":[55],"context-based":[56],"probability":[58],"model":[59,103,147],"that":[60,93,155],"extends":[61],"backbone-dependent":[63],"framework":[64],"by":[65,82],"integrating":[66],"additional":[67],"local":[68],"non-local":[70,120],"structural":[71],"sequence":[73],"information.":[74],"work,":[77],"states":[79],"are":[80,88],"defined":[81],"structure-based":[83],"clustering":[84],"conditional":[86],"probabilities":[87],"estimated":[89],"using":[90],"hierarchical":[91,146],"smoothing":[92],"combines":[94],"contextual":[95],"statistics":[96],"residue":[98],"specific":[99],"global":[100],"priors.":[101],"The":[102,160],"supports":[104],"multiple":[105],"context":[106],"definitions,":[107],"including":[108],"secondary":[109,178],"element":[111],"type,":[112],"coarse":[113],"biochemical":[114],"classes":[115],"neighboring":[117],"residues,":[118],"spatial":[121],"contacts.":[122],"We":[123],"evaluated":[124],"method":[126],"two":[128],"test":[129],"sets":[130],"compared":[132],"performance":[133],"against":[134],"one":[135],"state-of-the-art":[138],"dependent":[140],"libraries.":[141],"results,":[144],"achieved":[148,181],"comparable":[150],"to":[151],"or":[152,170],"modestly":[153],"exceeding":[154],"existing":[158],"library.":[159],"most":[161,183],"consistent":[162],"improvements":[163],"observed":[164],"were":[165],"three":[169],"four":[171],"chi(\u03c7)":[172],"angles.":[173],"Among":[174],"tested":[176],"contexts,":[177],"types":[180],"reliable":[184],"improvements.":[185]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
