{"id":"https://openalex.org/W1975118489","doi":"https://doi.org/10.1142/s0219720012420061","title":"IMPROVED EFFICIENCY IN CRYO-EM SECONDARY STRUCTURE TOPOLOGY DETERMINATION FROM INACCURATE DATA","display_name":"IMPROVED EFFICIENCY IN CRYO-EM SECONDARY STRUCTURE TOPOLOGY DETERMINATION FROM INACCURATE DATA","publication_year":2012,"publication_date":"2012-04-12","ids":{"openalex":"https://openalex.org/W1975118489","doi":"https://doi.org/10.1142/s0219720012420061","mag":"1975118489","pmid":"https://pubmed.ncbi.nlm.nih.gov/22809382"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720012420061","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720012420061","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","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/A5087997570","display_name":"Abhishek Biswas","orcid":"https://orcid.org/0000-0002-8074-2543"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"ABHISHEK BISWAS","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080683855","display_name":"Dong Si","orcid":"https://orcid.org/0000-0001-7039-2589"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DONG SI","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005997198","display_name":"Kamal Al Nasr","orcid":"https://orcid.org/0000-0001-8459-9070"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"KAMAL AL NASR","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102707396","display_name":"Desh Ranjan","orcid":null},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"DESH RANJAN","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101789500","display_name":"Mohammad Zubair","orcid":"https://orcid.org/0000-0002-5449-1779"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"MOHAMMAD ZUBAIR","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049641499","display_name":"Jing He","orcid":"https://orcid.org/0000-0002-7249-4746"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"JING HE","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5087997570"],"corresponding_institution_ids":["https://openalex.org/I81365321"],"apc_list":null,"apc_paid":null,"fwci":0.788,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.69610728,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"03","first_page":"1242006","last_page":"1242006"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9984999895095825,"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":0.9984999895095825,"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":0.998199999332428,"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":0.9977999925613403,"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/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6937609314918518},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.6832376718521118},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6429961919784546},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5577135682106018},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5456060767173767},{"id":"https://openalex.org/keywords/secondary-development","display_name":"Secondary development","score":0.5224456191062927},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.5199305415153503},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48998990654945374},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.45837047696113586},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4490531086921692},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.44489800930023193},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3347705900669098},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3168421983718872},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.282321572303772},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.16574892401695251},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11666157841682434},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11269208788871765},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10192182660102844},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.09994575381278992}],"concepts":[{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6937609314918518},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6832376718521118},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6429961919784546},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5577135682106018},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5456060767173767},{"id":"https://openalex.org/C2776460390","wikidata":"https://www.wikidata.org/wiki/Q7443832","display_name":"Secondary development","level":3,"score":0.5224456191062927},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.5199305415153503},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48998990654945374},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.45837047696113586},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4490531086921692},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.44489800930023193},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3347705900669098},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3168421983718872},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.282321572303772},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.16574892401695251},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11666157841682434},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11269208788871765},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10192182660102844},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.09994575381278992},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720012420061","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720012420061","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"},{"id":"pmid:22809382","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22809382","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320311672","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1558317748","https://openalex.org/W1966323820","https://openalex.org/W1969007008","https://openalex.org/W1979749477","https://openalex.org/W2006158980","https://openalex.org/W2008807736","https://openalex.org/W2013734705","https://openalex.org/W2020438176","https://openalex.org/W2026649417","https://openalex.org/W2029706450","https://openalex.org/W2046192291","https://openalex.org/W2048875539","https://openalex.org/W2072649575","https://openalex.org/W2080333910","https://openalex.org/W2096732301","https://openalex.org/W2117264607","https://openalex.org/W2124927299","https://openalex.org/W2142529984","https://openalex.org/W2152086886","https://openalex.org/W2155089380","https://openalex.org/W2156798505","https://openalex.org/W2165242943","https://openalex.org/W2178756744"],"related_works":["https://openalex.org/W2376688727","https://openalex.org/W2390140220","https://openalex.org/W2351277949","https://openalex.org/W2364382314","https://openalex.org/W2078778136","https://openalex.org/W2365371748","https://openalex.org/W2384960615","https://openalex.org/W2352848571","https://openalex.org/W2933325505","https://openalex.org/W2360889168"],"abstract_inverted_index":{"The":[0,59],"determination":[1],"of":[2,33,36,80,84,105,111,126,133,142,150,152,160,182,191,202,209],"the":[3,13,17,31,42,47,52,64,69,75,96,103,106,109,112,124,140,143,157,162,171,180,189,199,203,207,210],"secondary":[4,43,66,86,113,144,173,204],"structure":[5,15,87,114,174],"topology":[6,141,201],"is":[7,116,213],"a":[8,82,120,148],"critical":[9],"step":[10,27],"in":[11,77],"deriving":[12],"atomic":[14],"from":[16,22,41,46,63,68],"protein":[18,48],"density":[19,49],"map":[20,50],"obtained":[21],"electron":[23],"cryo-microscopy":[24],"technique.":[25],"This":[26,93],"often":[28],"relies":[29],"on":[30],"matching":[32],"two":[34],"sources":[35],"information.":[37],"One":[38],"source":[39,61,79],"comes":[40,62],"structures":[44,67,205],"detected":[45],"at":[51],"medium":[53],"resolution,":[54],"such":[55],"as":[56,154],"5-10":[57],"\u00c5.":[58],"other":[60],"predicted":[65,211],"amino":[70],"acid":[71],"sequence.":[72],"Due":[73],"to":[74,90,101,138,156,197],"inaccuracy":[76,110,208],"either":[78],"information,":[81],"pool":[83],"possible":[85],"positions":[88],"needs":[89],"be":[91],"sampled.":[92],"paper":[94],"studies":[95],"question,":[97],"that":[98,122],"is,":[99],"how":[100],"reduce":[102],"computation":[104],"mapping":[107],"when":[108,170,206],"predictions":[115],"considered.":[117,214],"We":[118,146,164],"present":[119],"method":[121],"combines":[123],"concept":[125],"dynamic":[127],"graph":[128],"with":[129],"our":[130],"previous":[131],"work":[132],"using":[134],"constrained":[135],"shortest":[136],"path":[137],"identify":[139,198],"structures.":[145],"show":[147,166],"reduction":[149],"34.55%":[151],"run-time":[153],"comparison":[155],"na\u00efve":[158],"way":[159],"handling":[161],"inaccuracies.":[163],"also":[165],"an":[167],"improved":[168],"accuracy":[169],"potential":[172,190],"errors":[175],"are":[176],"explicitly":[177],"sampled":[178],"verses":[179],"use":[181],"one":[183],"consensus":[184],"prediction.":[185],"Our":[186],"framework":[187],"demonstrated":[188],"developing":[192],"computationally":[193],"effective":[194],"exact":[195],"algorithms":[196],"optimal":[200],"data":[212]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}