{"id":"https://openalex.org/W2130274175","doi":"https://doi.org/10.1093/bioinformatics/bti1138","title":"Reconsidering complete search algorithms for protein backbone NMR assignment","display_name":"Reconsidering complete search algorithms for protein backbone NMR assignment","publication_year":2005,"publication_date":"2005-09-01","ids":{"openalex":"https://openalex.org/W2130274175","doi":"https://doi.org/10.1093/bioinformatics/bti1138","mag":"2130274175","pmid":"https://pubmed.ncbi.nlm.nih.gov/16204110"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti1138","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1138","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5088073215","display_name":"Olga Vitek","orcid":"https://orcid.org/0000-0003-1728-1104"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olga Vitek","raw_affiliation_strings":["Department of Statistics, Purdue University, West Lafayette, IN 47907, USA. ovitek@stat.purdue.edu","Department of Statistics, Purdue University West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Purdue University, West Lafayette, IN 47907, USA. ovitek@stat.purdue.edu","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Department of Statistics, Purdue University West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030579910","display_name":"Chris Bailey\u2010Kellogg","orcid":"https://orcid.org/0000-0003-1860-0912"},"institutions":[{"id":"https://openalex.org/I107672454","display_name":"Dartmouth College","ror":"https://ror.org/049s0rh22","country_code":"US","type":"education","lineage":["https://openalex.org/I107672454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris Bailey-Kellogg","raw_affiliation_strings":["Department of Computer Science, Dartmouth College, Hanover NH 03755 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Dartmouth College, Hanover NH 03755 USA","institution_ids":["https://openalex.org/I107672454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038449597","display_name":"Bruce \u0391. Craig","orcid":"https://orcid.org/0000-0001-9346-467X"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce Craig","raw_affiliation_strings":["Department of Statistics, Purdue University West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Purdue University West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088951176","display_name":"Paul Kuliniewicz","orcid":null},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Kuliniewicz","raw_affiliation_strings":["Department of Computer Sciences, Purdue University, West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084307280","display_name":"Jan V\u00edtek","orcid":"https://orcid.org/0000-0003-4052-3458"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jan Vitek","raw_affiliation_strings":["Department of Computer Sciences, Purdue University, West Lafayette, IN 47907, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, Purdue University, West Lafayette, IN 47907, USA","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8791,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.72209928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"suppl_2","first_page":"ii230","last_page":"ii236"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.91839998960495,"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":0.91839998960495,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.027000000700354576,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.008200000040233135,"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/algorithm","display_name":"Algorithm","score":0.6723930239677429},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.620759904384613},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5967441201210022},{"id":"https://openalex.org/keywords/ranging","display_name":"Ranging","score":0.520412802696228},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.4906824827194214},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4606248736381531},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.42370346188545227},{"id":"https://openalex.org/keywords/resonance","display_name":"Resonance (particle physics)","score":0.42097008228302},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13632124662399292}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6723930239677429},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.620759904384613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5967441201210022},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.520412802696228},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.4906824827194214},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4606248736381531},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.42370346188545227},{"id":"https://openalex.org/C139210041","wikidata":"https://www.wikidata.org/wiki/Q2145840","display_name":"Resonance (particle physics)","level":2,"score":0.42097008228302},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13632124662399292},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0},{"id":"https://openalex.org/C109214941","wikidata":"https://www.wikidata.org/wiki/Q18334","display_name":"Particle physics","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti1138","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti1138","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16204110","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16204110","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,"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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W95002730","https://openalex.org/W1498088837","https://openalex.org/W1498615754","https://openalex.org/W1507046264","https://openalex.org/W1520812788","https://openalex.org/W1964549109","https://openalex.org/W1990785823","https://openalex.org/W2005958413","https://openalex.org/W2092544746","https://openalex.org/W2097247365","https://openalex.org/W2125976362","https://openalex.org/W2130241756","https://openalex.org/W2136112599","https://openalex.org/W2151542228","https://openalex.org/W2169462961","https://openalex.org/W2277964952"],"related_works":["https://openalex.org/W4384112194","https://openalex.org/W2783354812","https://openalex.org/W4312958259","https://openalex.org/W2103009189","https://openalex.org/W4390813131","https://openalex.org/W2349383066","https://openalex.org/W4308259661","https://openalex.org/W4328132048","https://openalex.org/W1969901537","https://openalex.org/W2295196644"],"abstract_inverted_index":{"MOTIVATION:":[0],"Nuclear":[1],"magnetic":[2],"resonance":[3,25,34,143],"(NMR)":[4],"spectroscopy":[5],"is":[6,21,38,123,237,244,266,279],"widely":[7],"used":[8],"to":[9,31,41,60,88,117,129,195,227,269],"determine":[10],"and":[11,44,102,126,156,170,177,240],"analyze":[12],"protein":[13],"structures.":[14],"An":[15],"essential":[16],"step":[17],"in":[18,46,67,78,109,191,223,290],"NMR":[19,47],"studies":[20],"determining":[22],"the":[23,42,79,94,110,118,148,168,203,219,241,255,291,299],"backbone":[24,142],"assignment,":[26],"which":[27],"maps":[28],"individual":[29],"atoms":[30],"experimentally":[32],"measured":[33],"frequencies.":[35],"Performing":[36],"assignment":[37,73,242],"challenging":[39],"owing":[40],"noise":[43],"ambiguity":[45],"spectra.":[48],"Although":[49],"automated":[50],"procedures":[51],"have":[52,76],"been":[53],"investigated,":[54],"by-and-large":[55],"they":[56],"are":[57],"still":[58],"struggling":[59],"gain":[61],"acceptance":[62],"because":[63],"of":[64,72,100,112,175,202,257,261],"inherent":[65],"limits":[66],"scalability":[68],"and/or":[69],"unacceptable":[70],"levels":[71],"error.":[74],"To":[75],"confidence":[77],"results,":[80],"an":[81,283],"algorithm":[82,140,146,199],"should":[83],"be":[84,270,296],"complete,":[85],"i.e.":[86],"able":[87],"identify":[89],"all":[90,97,164,173,262],"solutions":[91,165],"consistent":[92,166],"with":[93,167,205],"data,":[95,169],"including":[96],"arbitrary":[98],"configurations":[99],"extra":[101,176],"missing":[103,178],"peaks.":[104],"The":[105,145,198,230,275,287],"ensuing":[106],"combinatorial":[107],"explosion":[108],"space":[111,150],"possible":[113],"assignments":[114,155],"has":[115,254],"led":[116],"perception":[119],"that":[120,249],"complete":[121,137,250],"search":[122,139,149,251],"hopelessly":[124],"inefficient":[125],"cannot":[127],"scale":[128],"realistic":[130],"datasets.":[131],"RESULTS:":[132],"This":[133],"paper":[134],"presents":[135],"a":[136],"branch-contract-and-bound":[138],"for":[141,234],"assignment.":[144],"controls":[147],"by":[151],"hierarchically":[152],"agglomerating":[153],"partial":[154],"employing":[157],"statistically":[158],"sound":[159],"pruning":[160],"criteria.":[161],"It":[162],"considers":[163],"uniformly":[171],"treats":[172],"combinations":[174],"data.":[179],"We":[180,208],"demonstrate":[181,248],"our":[182],"approach":[183],"on":[184,212],"experimental":[185],"data":[186,214],"from":[187,193,215,218,225,298],"five":[188],"proteins":[189,217],"ranging":[190,222],"size":[192,224],"70":[194],"154":[196],"residues.":[197,229],"assigns":[200],">95%":[201],"positions":[204],">98%":[206],"accuracy.":[207],"also":[209,295],"present":[210],"results":[211,247],"simulated":[213],"259":[216],"RefDB":[220],"database,":[221],"25":[226],"257":[228],"median":[231],"computation":[232],"time":[233],"these":[235],"cases":[236],"1":[238],"min,":[239],"accuracy":[243],">99%.":[245],"These":[246],"not":[252],"only":[253],"advantage":[256],"guaranteeing":[258],"fair":[259],"treatment":[260],"feasible":[263],"solutions,":[264],"but":[265],"efficient":[267],"enough":[268],"employed":[271],"effectively":[272],"inpractice.":[273],"AVAILABILITY:":[274],"MBA(2)":[276],"software":[277,285],"package":[278],"made":[280],"available":[281],"under":[282],"open-source":[284],"license.":[286],"datasets":[288],"featured":[289],"Results":[292],"section":[293],"can":[294],"obtained":[297],"contact":[300],"author.":[301]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
