{"id":"https://openalex.org/W1985335558","doi":"https://doi.org/10.1093/comjnl/bxp120","title":"NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments","display_name":"NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments","publication_year":2010,"publication_date":"2010-01-06","ids":{"openalex":"https://openalex.org/W1985335558","doi":"https://doi.org/10.1093/comjnl/bxp120","mag":"1985335558","pmid":"https://pubmed.ncbi.nlm.nih.gov/25580019"},"language":"en","primary_location":{"id":"doi:10.1093/comjnl/bxp120","is_oa":false,"landing_page_url":"https://doi.org/10.1093/comjnl/bxp120","pdf_url":null,"source":{"id":"https://openalex.org/S44643521","display_name":"The Computer Journal","issn_l":"0010-4620","issn":["0010-4620","1460-2067"],"is_oa":false,"is_in_doaj":false,"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":"The Computer Journal","raw_type":"journal-article"},"type":"article","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/A5022556437","display_name":"Mehmet Serkan Apayd\u0131n","orcid":"https://orcid.org/0000-0002-4707-8994"},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"M. S. Apaydin","raw_affiliation_strings":["Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0131stanbul, Turkey","Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0130stanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0131stanbul, Turkey","institution_ids":["https://openalex.org/I134235054"]},{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0130stanbul, Turkey","institution_ids":["https://openalex.org/I134235054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030544686","display_name":"B\u00fclent \u00c7atay","orcid":"https://orcid.org/0000-0001-5950-3321"},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"B. Catay","raw_affiliation_strings":["Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0131stanbul, Turkey","Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0130stanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0131stanbul, Turkey","institution_ids":["https://openalex.org/I134235054"]},{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Orhanl\u0131 Tuzla, 34956 \u0130stanbul, Turkey","institution_ids":["https://openalex.org/I134235054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113820120","display_name":"Nicholas Patrick","orcid":null},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N. Patrick","raw_affiliation_strings":["Department of Computer Science, Duke University, Durham, NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046723017","display_name":"Bruce R. Donald","orcid":"https://orcid.org/0000-0001-6884-4398"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]},{"id":"https://openalex.org/I4210153043","display_name":"Duke University Hospital","ror":"https://ror.org/04bct7p84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876","https://openalex.org/I4210144876","https://openalex.org/I4210153043"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. R. Donald","raw_affiliation_strings":["Department of Computer Science, Duke University, Durham, NC 27708, USA ; Department of Biochemistry, Duke University Medical Center, Durham, NC 27708, USA","Department of Biochemistry, Duke University Medical Center, Durham, NC 27708, USA","Department of Computer Science, Duke University, Durham, NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, NC 27708, USA ; Department of Biochemistry, Duke University Medical Center, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210126298"]},{"raw_affiliation_string":"Department of Biochemistry, Duke University Medical Center, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I4210126298","https://openalex.org/I4210153043"]},{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022556437"],"corresponding_institution_ids":["https://openalex.org/I134235054"],"apc_list":{"value":2635,"currency":"GBP","value_usd":3232},"apc_paid":null,"fwci":1.369,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.78890706,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"54","issue":"5","first_page":"708","last_page":"716"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9941999912261963,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9941999912261963,"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":0.9929999709129333,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9922999739646912,"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/binary-number","display_name":"Binary number","score":0.6753139495849609},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.5305771231651306},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.449348509311676},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39950916171073914},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3369064927101135},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.32287701964378357},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2752467393875122},{"id":"https://openalex.org/keywords/arithmetic","display_name":"Arithmetic","score":0.1316058337688446},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11578604578971863}],"concepts":[{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.6753139495849609},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.5305771231651306},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.449348509311676},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39950916171073914},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3369064927101135},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.32287701964378357},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2752467393875122},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.1316058337688446},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11578604578971863}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/comjnl/bxp120","is_oa":false,"landing_page_url":"https://doi.org/10.1093/comjnl/bxp120","pdf_url":null,"source":{"id":"https://openalex.org/S44643521","display_name":"The Computer Journal","issn_l":"0010-4620","issn":["0010-4620","1460-2067"],"is_oa":false,"is_in_doaj":false,"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":"The Computer Journal","raw_type":"journal-article"},{"id":"pmid:25580019","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25580019","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":"The computer journal","raw_type":null},{"id":"pmh:oai:europepmc.org:3257768","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4287374","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8560422051","display_name":null,"funder_award_id":"R01 GM065982","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"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":19,"referenced_works":["https://openalex.org/W1885159080","https://openalex.org/W1964549109","https://openalex.org/W1967230337","https://openalex.org/W1970208847","https://openalex.org/W2017478462","https://openalex.org/W2047000799","https://openalex.org/W2061791555","https://openalex.org/W2073486807","https://openalex.org/W2080837519","https://openalex.org/W2085565764","https://openalex.org/W2092544746","https://openalex.org/W2101574921","https://openalex.org/W2116376617","https://openalex.org/W2135307619","https://openalex.org/W2142026881","https://openalex.org/W2153996799","https://openalex.org/W2154821473","https://openalex.org/W2159121958","https://openalex.org/W2319226565"],"related_works":["https://openalex.org/W2935759653","https://openalex.org/W3105167352","https://openalex.org/W54078636","https://openalex.org/W1925942709","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W4298824844","https://openalex.org/W2082154838","https://openalex.org/W2109912052","https://openalex.org/W1711527768"],"abstract_inverted_index":{"Nuclear":[0,111],"magnetic":[1],"resonance":[2,165],"(NMR)":[3],"spectroscopy":[4],"is":[5,29,55,240,267],"an":[6],"important":[7,22],"experimental":[8],"technique":[9,205],"that":[10],"allows":[11,236,255],"one":[12],"to":[13,35,43,57,221,257,270],"study":[14,65],"protein":[15,26,53],"structure":[16,27],"and":[17,60,70,105,152,178,181,189,243,266],"dynamics":[18],"in":[19,24,63,127],"solution.":[20],"An":[21,156],"bottleneck":[23],"NMR":[25,33,117,164],"determination":[28],"the":[30,36,48,58,64,121,184,246,259],"assignment":[31,40,79,223],"of":[32,50,66,186,196,262,274],"peaks":[34],"corresponding":[37],"nuclei.":[38],"Structure-based":[39],"(SBA)":[41],"aims":[42],"solve":[44],"this":[45],"problem":[46,80],"with":[47,81],"help":[49],"a":[51,77],"template":[52],"which":[54,87,199],"homologous":[56],"target":[59],"has":[61],"applications":[62],"structure\u2013activity":[67],"relationship,":[68],"protein\u2013protein":[69],"protein\u2013ligand":[71],"interactions.":[72],"We":[73,202],"formulate":[74],"SBA":[75],"as":[76,210,212,248,250,278],"linear":[78],"additional":[82,279],"nuclear":[83,92,158],"overhauser":[84],"effect":[85],"constraints,":[86],"can":[88,244],"be":[89],"solved":[90],"within":[91],"vector":[93,159],"replacement's":[94],"(NVR)":[95],"framework":[96],"(Langmead,":[97],"C.,":[98],"Yan,":[99],"A.,":[100],"Lilien,":[101],"R.,":[102],"Wang,":[103],"L.":[104],"Donald,":[106,153],"B.":[107,154],"(2003)":[108],"A":[109],"Polynomial-Time":[110],"Vector":[112],"Replacement":[113],"Algorithm":[114],"for":[115,162],"Automated":[116],"Resonance":[118],"Assignments.":[119],"Proc.":[120],"7th":[122],"Annual":[123],"Int.":[124],"Conf.":[125],"Research":[126],"Computational":[128],"Molecular":[129],"Biology":[130],"(RECOMB),":[131],"Berlin,":[132],"Germany,":[133],"April":[134],"10\u201313,":[135],"pp.":[136,148],"176\u2013187.":[137],"ACM":[138],"Press,":[139],"New":[140],"York,":[141],"NY.":[142],"J.":[143,167],"Comp.":[144],"Bio.,":[145],"(2004),":[146],"11,":[147],"277\u2013298;":[149],"Langmead,":[150],"C.":[151],"(2004)":[155],"expectation/maximization":[157],"replacement":[160],"algorithm":[161],"automated":[163],"assignments.":[166,238,252],"Biomol.":[168],"NMR,":[169],"29,":[170],"111\u2013138).":[171],"Our":[172,217,234],"approach":[173,235],"uses":[174],"NVR's":[175,207,222,226],"scoring":[176],"function":[177],"data":[179,208,264],"types":[180],"also":[182,241],"gives":[183],"option":[185],"using":[187],"CH":[188],"NH":[190,197],"residual":[191],"dipolar":[192],"coupling":[193],"(RDCs),":[194],"instead":[195],"RDCs":[198],"NVR":[200],"requires.":[201],"test":[203,227],"our":[204],"on":[206,213,225,231],"set":[209],"well":[211,249],"four":[214],"new":[215,272],"proteins.":[216,233],"results":[218],"are":[219],"comparable":[220],"accuracy":[224],"set,":[228],"but":[229],"higher":[230],"novel":[232],"partial":[237],"It":[239],"complete":[242],"return":[245],"optimum":[247],"near-optimum":[251],"Furthermore,":[253],"it":[254],"us":[256],"analyze":[258],"information":[260],"content":[261],"each":[263],"type":[265],"easily":[268],"extendable":[269],"accept":[271],"forms":[273],"input":[275],"data,":[276],"such":[277],"RDCs.":[280]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
