{"id":"https://openalex.org/W2018816581","doi":"https://doi.org/10.1145/2506583.2506705","title":"A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps","display_name":"A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps","publication_year":2013,"publication_date":"2013-09-22","ids":{"openalex":"https://openalex.org/W2018816581","doi":"https://doi.org/10.1145/2506583.2506705","mag":"2018816581"},"language":"en","primary_location":{"id":"doi:10.1145/2506583.2506705","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506705","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-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/A5005997198","display_name":"Kamal Al Nasr","orcid":"https://orcid.org/0000-0001-8459-9070"},"institutions":[{"id":"https://openalex.org/I75256744","display_name":"Tennessee State University","ror":"https://ror.org/01fpczx89","country_code":"US","type":"education","lineage":["https://openalex.org/I75256744"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kamal Al Nasr","raw_affiliation_strings":["Dept. of Computer Science, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209","Dept. of Computer Science, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209","institution_ids":["https://openalex.org/I75256744"]},{"raw_affiliation_string":"Dept. of Computer Science, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209#TAB#","institution_ids":["https://openalex.org/I75256744"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100443709","display_name":"Lin Chen","orcid":"https://orcid.org/0000-0002-1108-4735"},"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":"Lin Chen","raw_affiliation_strings":["Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","Department of Computer Science, Old Dominion University, Norfolk, VA 23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529","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":["Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","Department of Computer Science, Old Dominion University, Norfolk, VA 23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529","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":"M. Zubair","raw_affiliation_strings":["Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","Department of Computer Science, Old Dominion University, Norfolk, VA 23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529","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":["Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","Department of Computer Science, Old Dominion University, Norfolk, VA 23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529","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":["Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","Department of Computer Science, Old Dominion University, Norfolk, VA 23529"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, VA 23529","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.9525,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.89735614,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"749","last_page":"755"},"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":0.9979000091552734,"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":0.9979000091552734,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9973999857902527,"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":0.9955000281333923,"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":0.7056174278259277},{"id":"https://openalex.org/keywords/shortest-path-problem","display_name":"Shortest path problem","score":0.6174673438072205},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5757783055305481},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.564647376537323},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5159947872161865},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.49381789565086365},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.46338164806365967},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43870607018470764},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.38353174924850464},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.25772804021835327},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2518014907836914},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.07331648468971252}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7056174278259277},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.6174673438072205},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5757783055305481},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.564647376537323},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5159947872161865},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.49381789565086365},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.46338164806365967},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43870607018470764},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.38353174924850464},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25772804021835327},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2518014907836914},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.07331648468971252},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2506583.2506705","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2506583.2506705","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1963844724","https://openalex.org/W1966323820","https://openalex.org/W1979147675","https://openalex.org/W1979749477","https://openalex.org/W1994086483","https://openalex.org/W2006158980","https://openalex.org/W2012798337","https://openalex.org/W2034527511","https://openalex.org/W2035460215","https://openalex.org/W2046192291","https://openalex.org/W2048875539","https://openalex.org/W2053880783","https://openalex.org/W2054889627","https://openalex.org/W2080333910","https://openalex.org/W2089966385","https://openalex.org/W2094918130","https://openalex.org/W2096495474","https://openalex.org/W2096732301","https://openalex.org/W2111070241","https://openalex.org/W2112643276","https://openalex.org/W2116007667","https://openalex.org/W2117264607","https://openalex.org/W2117756276","https://openalex.org/W2128801478","https://openalex.org/W2129909716","https://openalex.org/W2133442602","https://openalex.org/W2141049683","https://openalex.org/W2144108054","https://openalex.org/W2147791333","https://openalex.org/W2149476505","https://openalex.org/W2152086886","https://openalex.org/W2153187042","https://openalex.org/W2171700940"],"related_works":["https://openalex.org/W2086397253","https://openalex.org/W2133122801","https://openalex.org/W600422426","https://openalex.org/W2007156430","https://openalex.org/W3081478936","https://openalex.org/W2785612136","https://openalex.org/W2099529706","https://openalex.org/W1988224651","https://openalex.org/W2096179639","https://openalex.org/W2560916850"],"abstract_inverted_index":{"Although":[0],"many":[1],"electron":[2],"density":[3],"maps":[4],"have":[5],"been":[6],"produced":[7],"into":[8],"the":[9,18,30,47,56,59,78,82,92,102,109,114,125],"medium":[10],"resolutions,":[11],"it":[12],"is":[13,111],"still":[14],"challenging":[15],"to":[16,64,90],"derive":[17],"atomic":[19,35],"structure":[20,36,43,61],"from":[21,113],"such":[22],"volumetric":[23],"data.":[24],"Current":[25],"methods":[26],"primarily":[27],"rely":[28],"on":[29],"availability":[31],"of":[32,49,58,76,108,119,130],"an":[33,88,131],"existing":[34,132],"for":[37,44],"fitting":[38],"or":[39],"a":[40,51,97],"homologous":[41],"template":[42],"modeling.":[45],"In":[46,68],"process":[48],"developing":[50],"template-free,":[52],"de":[53],"novo,":[54],"method,":[55],"topology":[57],"secondary":[60],"elements":[62],"need":[63],"be":[65],"resolved":[66],"first.":[67],"this":[69],"paper,":[70],"we":[71],"extend":[72],"our":[73],"previous":[74],"algorithm":[75,100,123],"finding":[77],"optimal":[79],"solution":[80],"in":[81],"constraint":[83],"graph":[84],"problem.":[85],"We":[86],"illustrate":[87],"approach":[89],"obtain":[91],"top-K":[93],"topologies":[94],"by":[95],"combining":[96],"dynamic":[98],"programming":[99],"with":[101],"K-shortest":[103],"path":[104],"algorithm.":[105],"The":[106,122],"effectiveness":[107],"algorithms":[110],"demonstrated":[112],"test":[115],"using":[116],"three":[117],"datasets":[118],"different":[120],"nature.":[121],"improves":[124],"accuracy,":[126],"space":[127],"and":[128],"time":[129],"method.":[133]},"counts_by_year":[{"year":2016,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}