{"id":"https://openalex.org/W2968304446","doi":"https://doi.org/10.1109/tcbb.2019.2934102","title":"A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model","display_name":"A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model","publication_year":2019,"publication_date":"2019-08-13","ids":{"openalex":"https://openalex.org/W2968304446","doi":"https://doi.org/10.1109/tcbb.2019.2934102","mag":"2968304446","pmid":"https://pubmed.ncbi.nlm.nih.gov/31403440"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2934102","doi":"https://doi.org/10.1109/tcbb.2019.2934102","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2934102","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","dongbi-b","doyens","jufo-2","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2968304446"],"child_works_count":0,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"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/A5085193162","display_name":"Hsin-Hung Chou","orcid":"https://orcid.org/0000-0003-1627-9598","observed_orcids":["https://orcid.org/0000-0003-1627-9598"]},"institutions":[{"id":"https://openalex.org/I80327900","display_name":"Chang Jung Christian University","ror":"https://ror.org/02s3d7j94","country_code":"TW","type":"education","lineage":["https://openalex.org/I80327900"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Hsin-Hung Chou","raw_affiliation_strings":["Chang Jung Christian University, Tainan, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-1627-9598","affiliations":[{"raw_affiliation_string":"Chang Jung Christian University, Tainan, Taiwan","institution_ids":["https://openalex.org/I80327900"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100860974","display_name":"Ching-Tien Hsu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Ching-Tien Hsu","raw_affiliation_strings":["Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055424928","display_name":"Li-Hsuan Chen","orcid":"https://orcid.org/0009-0007-6528-7064","observed_orcids":["https://orcid.org/0009-0007-6528-7064"]},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Li-Hsuan Chen","raw_affiliation_strings":["Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yue-Cheng Lin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yue-Cheng Lin","raw_affiliation_strings":["Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103047340","display_name":"Sun\u2010Yuan Hsieh","orcid":"https://orcid.org/0000-0003-4746-3179","observed_orcids":["https://orcid.org/0000-0003-4746-3179"]},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Sun-Yuan Hsieh","raw_affiliation_strings":["Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-4746-3179","affiliations":[{"raw_affiliation_string":"Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan","institution_ids":["https://openalex.org/I91807558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2045,"currency":"USD","value_usd":2045},"apc_paid":null,"fwci":0.0728,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.33073784,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"18","issue":"2","first_page":"455","last_page":"462"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9897000193595886,"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":0.9897000193595886,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.00430000014603138,"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/T11269","display_name":"Algorithms and Data Compression","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.8240000009536743},{"id":"https://openalex.org/keywords/hydrophobic-polar-model","display_name":"hydrophobic-polar model","score":0.9670000076293945},{"id":"https://openalex.org/keywords/branch-and-bound","display_name":"branch and bound","score":0.9829999804496765},{"id":"https://openalex.org/keywords/np-completeness","display_name":"NP-completeness","score":0.8629999756813049},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"energy minimization","score":0.8379999995231628},{"id":"https://openalex.org/keywords/combinatorial-optimization","display_name":"combinatorial optimization","score":0.6259999871253967}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7027014493942261},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6595758199691772},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6298824548721313},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.590745747089386},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5605101585388184},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4990057945251465},{"id":"https://openalex.org/C2781204021","wikidata":"https://www.wikidata.org/wiki/Q6497091","display_name":"Lattice (music)","level":2,"score":0.4783289432525635},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4539801776409149},{"id":"https://openalex.org/C93693863","wikidata":"https://www.wikidata.org/wiki/Q897659","display_name":"Branch and bound","level":2,"score":0.43039655685424805},{"id":"https://openalex.org/C32598905","wikidata":"https://www.wikidata.org/wiki/Q6497130","display_name":"Lattice protein","level":3,"score":0.4175284504890442},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3419674038887024},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3248059153556824},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31871187686920166},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1972038447856903},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1742013692855835},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08275452256202698},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2934102","doi":"https://doi.org/10.1109/tcbb.2019.2934102","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2934102","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","dongbi-b","doyens","jufo-2","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31403440","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31403440","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1524028948","display_name":null,"funder_award_id":"MOST 105-2221-006-164-MY3","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G8379033854","display_name":"The Hamiltonian Properties of Regular Graph under the Conditional Fault Model","funder_award_id":"MOST103-2218-E006-019-MY3","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"}],"funders":[{"id":"https://openalex.org/F4320322795","display_name":"Ministry of Science and Technology, Taiwan","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1491063910","https://openalex.org/W1501449128","https://openalex.org/W1519786096","https://openalex.org/W1640378004","https://openalex.org/W1981448105","https://openalex.org/W1984527736","https://openalex.org/W1988401986","https://openalex.org/W2002098814","https://openalex.org/W2012217649","https://openalex.org/W2013842855","https://openalex.org/W2062175659","https://openalex.org/W2072042890","https://openalex.org/W2079492386","https://openalex.org/W2080382112","https://openalex.org/W2088530697","https://openalex.org/W2098387581","https://openalex.org/W2107941094","https://openalex.org/W2114899912","https://openalex.org/W2139415631","https://openalex.org/W2145387267","https://openalex.org/W2150736837","https://openalex.org/W2154929945","https://openalex.org/W2611927968","https://openalex.org/W2907227701","https://openalex.org/W4388325150"],"related_works":["https://openalex.org/W1501449128","https://openalex.org/W2792037970","https://openalex.org/W2159296057","https://openalex.org/W2040050205","https://openalex.org/W2319086645","https://openalex.org/W2109822494","https://openalex.org/W7097814859","https://openalex.org/W2378187602","https://openalex.org/W1565471116","https://openalex.org/W2053353480"],"abstract_inverted_index":{"The":[0,32],"protein":[1,22],"folding":[2,23],"problem":[3,53],"(PFP)":[4],"is":[5,24],"an":[6],"important":[7],"issue":[8],"in":[9,34,87],"bioinformatics":[10],"and":[11],"biochemical":[12],"physics.":[13],"One":[14],"of":[15,21],"the":[16,25,35,47,52,80,85,88,102],"most":[17,62],"widely":[18],"studied":[19],"models":[20],"hydrophobic-polar":[26],"(HP)":[27],"model":[28,40],"introduced":[29],"by":[30],"Dill.":[31],"PFP":[33,86],"three-dimensional":[36],"(3D)":[37],"lattice":[38,90],"HP":[39,91],"has":[41],"been":[42],"shown":[43],"to":[44,83],"be":[45],"NP-complete;":[46],"proposed":[48,99],"algorithms":[49],"for":[50,61],"solving":[51],"can":[54],"therefore":[55],"only":[56],"find":[57],"near-optimal":[58],"energy":[59],"structures":[60],"long":[63],"benchmark":[64,96],"sequences":[65],"within":[66,107],"acceptable":[67],"time":[68],"periods.":[69],"In":[70],"this":[71],"paper,":[72],"we":[73],"propose":[74],"a":[75],"novel":[76],"algorithm":[77,100],"based":[78],"on":[79],"branch-and-bound":[81],"approach":[82],"solve":[84],"3D":[89],"model.":[92],"For":[93],"10":[94],"48-monomer":[95],"sequences,":[97],"our":[98],"finds":[101],"lowest":[103],"energies":[104],"so":[105],"far":[106],"comparable":[108],"computation":[109],"times":[110],"than":[111],"previous":[112],"methods.":[113]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2019-08-22T00:00:00"}
