{"id":"https://openalex.org/W3189467602","doi":"https://doi.org/10.1145/3459930.3469491","title":"Hybridized distance- and contact- based hierarchical protein structure modeling using DConStruct","display_name":"Hybridized distance- and contact- based hierarchical protein structure modeling using DConStruct","publication_year":2021,"publication_date":"2021-07-30","ids":{"openalex":"https://openalex.org/W3189467602","doi":"https://doi.org/10.1145/3459930.3469491","mag":"3189467602"},"language":"en","primary_location":{"id":"doi:10.1145/3459930.3469491","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3459930.3469491","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5041995175","display_name":"Rahmatullah Roche","orcid":"https://orcid.org/0009-0005-8593-8210"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahmatullah Roche","raw_affiliation_strings":["Auburn University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101844843","display_name":"Sutanu Bhattacharya","orcid":"https://orcid.org/0000-0002-3780-5174"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sutanu Bhattacharya","raw_affiliation_strings":["Auburn University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Auburn University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University","institution_ids":["https://openalex.org/I82497590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I82497590"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07320803,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9805999994277954,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6161595582962036},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5852183103561401},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.47694888710975647},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.4582066535949707},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.44678205251693726},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.44460976123809814},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4349152445793152},{"id":"https://openalex.org/keywords/casp","display_name":"CASP","score":0.4301197826862335},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42907002568244934},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.42221707105636597},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4042423665523529},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3759261667728424},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2117980420589447},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19826331734657288},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10761970281600952}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6161595582962036},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5852183103561401},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.47694888710975647},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4582066535949707},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.44678205251693726},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.44460976123809814},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4349152445793152},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.4301197826862335},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42907002568244934},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.42221707105636597},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4042423665523529},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3759261667728424},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2117980420589447},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19826331734657288},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10761970281600952},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3459930.3469491","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3459930.3469491","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.49000000953674316,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G4881500090","display_name":null,"funder_award_id":"(IIS2030722, DBI1942692)","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5781645967","display_name":null,"funder_award_id":"(R35GM138146)","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":1,"referenced_works":["https://openalex.org/W3132225743"],"related_works":["https://openalex.org/W2928838901","https://openalex.org/W2946599741","https://openalex.org/W2147472674","https://openalex.org/W2561391236","https://openalex.org/W1888349473","https://openalex.org/W2136856901","https://openalex.org/W1567853508","https://openalex.org/W4225106352","https://openalex.org/W3165545667","https://openalex.org/W3171039768"],"abstract_inverted_index":{"Crystallography":[0],"and":[1,94,103,125,156],"NMR":[2],"system":[3],"(CNS)":[4],"is":[5,26,176],"a":[6,66,99,115,135],"widely":[7],"used":[8],"method":[9,31,71,146],"for":[10,36,53,153],"predicting":[11],"3D":[12],"structures":[13],"of":[14,114],"protein":[15,68,117],"from":[16,40,98],"inter-residue":[17,92],"distance":[18],"or":[19],"contact":[20],"maps.":[21],"However,":[22],"the":[23,58,87,110,130,150,170],"decade-old":[24],"CNS":[25,52],"an":[27],"experimental":[28,41],"structure":[29,47,54,69,132],"determination":[30],"that":[32,143],"was":[33],"originally":[34],"developed":[35],"solving":[37],"macromolecular":[38],"geometry":[39],"restraints,":[42],"as":[43],"opposed":[44],"to":[45,121,160],"predictive":[46,79],"modeling.":[48],"Thus,":[49],"relying":[50],"on":[51],"modeling":[55,70,80],"may":[56],"undermine":[57],"ab":[59],"initio":[60],"folding":[61,151],"performance.":[62],"Here":[63],"we":[64],"propose":[65],"CNS-free":[67],"called":[72],"DConStruct":[73,106,165],"[1],":[74],"which":[75],"performs":[76],"3-stage":[77],"hierarchical":[78],"with":[81],"iterative":[82],"self-correction":[83],"driven":[84],"purely":[85],"by":[86,91],"geometric":[88],"restraints":[89],"induced":[90],"interactions":[93,127],"secondary":[95,104,131],"structures.":[96],"Starting":[97],"residue-residue":[100],"interaction":[101],"map":[102],"structure,":[105],"can":[107,147],"hierarchically":[108],"estimate":[109],"correct":[111],"overall":[112],"fold":[113],"target":[116],"in":[118,134],"coarse-grained":[119],"mode":[120],"progressively":[122],"optimize":[123],"local":[124],"non-local":[126],"while":[128],"enhancing":[129],"topology":[133],"self-correcting":[136],"manner.":[137],"Multiple":[138],"large-scale":[139],"benchmarking":[140],"experiments":[141],"show":[142],"our":[144],"proposed":[145],"substantially":[148],"improve":[149],"accuracy":[152],"both":[154],"soluble":[155],"membrane":[157],"proteins":[158],"compared":[159],"state-of-the-art":[161],"approaches.":[162],"The":[163],"open-source":[164],"software":[166],"package,":[167],"licensed":[168],"under":[169],"GNU":[171],"General":[172],"Public":[173],"License":[174],"v3,":[175],"freely":[177],"available":[178],"at":[179],"https://github.com/Bhattacharya-Lab/DConStruct.":[180]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}