{"id":"https://openalex.org/W2124927299","doi":"https://doi.org/10.1142/s0219720008003357","title":"DERIVING TOPOLOGY AND SEQUENCE ALIGNMENT FOR THE HELIX SKELETON IN LOW-RESOLUTION PROTEIN DENSITY MAPS","display_name":"DERIVING TOPOLOGY AND SEQUENCE ALIGNMENT FOR THE HELIX SKELETON IN LOW-RESOLUTION PROTEIN DENSITY MAPS","publication_year":2008,"publication_date":"2008-02-01","ids":{"openalex":"https://openalex.org/W2124927299","doi":"https://doi.org/10.1142/s0219720008003357","mag":"2124927299"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720008003357","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003357","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-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/A5082133960","display_name":"Yonggang Lu","orcid":"https://orcid.org/0000-0001-8926-2039"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"YONGGANG LU","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA","Department of Computer Science, New Mexico State University, Las Cruces NM, 88003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA","institution_ids":["https://openalex.org/I10052268"]},{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces NM, 88003, USA","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049641499","display_name":"Jing He","orcid":"https://orcid.org/0000-0002-7249-4746"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"JING HE","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA","Department of Computer Science, New Mexico State University, Las Cruces NM, 88003, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA","institution_ids":["https://openalex.org/I10052268"]},{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, Las Cruces NM, 88003, USA","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089757137","display_name":"Charlie E. M. Strauss","orcid":"https://orcid.org/0000-0003-3639-4673"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"CHARLIE E. M. STRAUSS","raw_affiliation_strings":["Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.488,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.94053799,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"06","issue":"01","first_page":"183","last_page":"201"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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":0.998199999332428,"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":0.9979000091552734,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.6817271709442139},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6128343343734741},{"id":"https://openalex.org/keywords/skeleton","display_name":"Skeleton (computer programming)","score":0.6010642647743225},{"id":"https://openalex.org/keywords/helix","display_name":"Helix (gastropod)","score":0.5436157584190369},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5394800901412964},{"id":"https://openalex.org/keywords/decoy","display_name":"Decoy","score":0.5190834999084473},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.49558961391448975},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.47733384370803833},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.45074090361595154},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42304807901382446},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.41948679089546204},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3832392990589142},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3319374918937683},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.29528769850730896},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2336845099925995},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20271897315979004},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20044639706611633},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17189499735832214},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.13429388403892517},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09953883290290833}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6817271709442139},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6128343343734741},{"id":"https://openalex.org/C18969341","wikidata":"https://www.wikidata.org/wiki/Q1169129","display_name":"Skeleton (computer programming)","level":2,"score":0.6010642647743225},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.5436157584190369},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5394800901412964},{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.5190834999084473},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.49558961391448975},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.47733384370803833},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.45074090361595154},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42304807901382446},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.41948679089546204},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3832392990589142},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3319374918937683},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.29528769850730896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2336845099925995},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20271897315979004},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20044639706611633},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17189499735832214},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.13429388403892517},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09953883290290833},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1142/s0219720008003357","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003357","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332186","display_name":"Defense Threat Reduction Agency","ror":"https://ror.org/04tz64554"},{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1530286200","https://openalex.org/W1548178570","https://openalex.org/W1550517035","https://openalex.org/W1555722003","https://openalex.org/W1557027001","https://openalex.org/W1963844724","https://openalex.org/W1966323820","https://openalex.org/W2005129556","https://openalex.org/W2006158980","https://openalex.org/W2013792107","https://openalex.org/W2025641516","https://openalex.org/W2048937426","https://openalex.org/W2052963427","https://openalex.org/W2077466611","https://openalex.org/W2089966385","https://openalex.org/W2097031841","https://openalex.org/W2107538253","https://openalex.org/W2108067237","https://openalex.org/W2108107014","https://openalex.org/W2111070241","https://openalex.org/W2116340182","https://openalex.org/W2149476505","https://openalex.org/W2150987569","https://openalex.org/W2152086886","https://openalex.org/W2155089380","https://openalex.org/W2171700940"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W1482324242","https://openalex.org/W1985408726","https://openalex.org/W2084367350","https://openalex.org/W2088487249","https://openalex.org/W2187357871","https://openalex.org/W2414840205","https://openalex.org/W1741740882"],"abstract_inverted_index":{"Cryoelectron":[0],"microscopy":[1],"(cryoEM)":[2],"is":[3,20,39,183,204],"an":[4],"experimental":[5],"technique":[6,19],"to":[7,22,68,97,193],"determine":[8],"the":[9,33,36,53,57,60,70,76,82,86,90,106,111,119,122,140,145,154,159,162,170,180,195,201],"three-dimensional":[10],"(3D)":[11],"structure":[12,37,94],"of":[13,35,41,56,85,121,132,139,144,161,197],"large":[14],"protein":[15,24,58,61],"complexes.":[16],"Currently,":[17],"this":[18],"able":[21],"generate":[23],"density":[25,62],"maps":[26],"at":[27,31],"6\u20139":[28],"\u00c5":[29],"resolution,":[30],"which":[32],"skeleton":[34,77,87,107,123,163],"(which":[38],"composed":[40],"\u03b1-helices":[42],"and":[43,72,102],"\u03b2-sheets)":[44],"can":[45],"be":[46],"visualized.":[47],"As":[48],"a":[49,66,99,127,166,184,188],"step":[50],"towards":[51],"predicting":[52],"entire":[54],"backbone":[55],"from":[59,130],"map,":[63],"we":[64],"developed":[65],"method":[67,80,96,112,186,192],"predict":[69],"topology":[71,101,129,181],"sequence":[73,103],"alignment":[74,104,141],"for":[75,105,142,169],"helices.":[78,108],"Our":[79,176],"combines":[81],"geometrical":[83],"information":[84],"helices":[88,124,147,164],"with":[89,113],"Rosetta":[91],"ab":[92],"initio":[93],"prediction":[95],"derive":[98],"consensus":[100],"We":[109,156],"tested":[110],"60":[114],"proteins.":[115],"For":[116],"45":[117],"proteins,":[118],"majority":[120],"were":[125,148],"assigned":[126,146],"correct":[128],"one":[131],"our":[133],"top":[134],"ten":[135],"predictions.":[136],"The":[137],"offsets":[138],"most":[143],"within":[149],"\u00b12":[150],"amino":[151],"acids":[152],"in":[153],"sequence.":[155],"also":[157],"analyzed":[158],"use":[160],"as":[165],"clustering":[167,182,191],"tool":[168],"decoy":[171,202],"structures":[172],"generated":[173],"by":[174],"Rosetta.":[175],"comparison":[177],"suggests":[178],"that":[179],"better":[185],"than":[187],"general":[189],"overlap":[190],"enrich":[194],"ranking":[196],"decoys,":[198],"particularly":[199],"when":[200],"pool":[203],"small.":[205]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2016-06-24T00:00:00"}