{"id":"https://openalex.org/W2747777001","doi":"https://doi.org/10.1145/3107411.3107501","title":"A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps","display_name":"A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2747777001","doi":"https://doi.org/10.1145/3107411.3107501","mag":"2747777001"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107501","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107501","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health 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/A5037079603","display_name":"Peter Collins","orcid":"https://orcid.org/0000-0002-3510-3398"},"institutions":[{"id":"https://openalex.org/I4210138624","display_name":"University of Washington Bothell","ror":"https://ror.org/02ygzhr13","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210138624"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter Collins","raw_affiliation_strings":["University of Washington Bothell, Bothell, WA, USA"],"affiliations":[{"raw_affiliation_string":"University of Washington Bothell, Bothell, WA, USA","institution_ids":["https://openalex.org/I4210138624"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080683855","display_name":"Dong Si","orcid":"https://orcid.org/0000-0001-7039-2589"},"institutions":[{"id":"https://openalex.org/I4210138624","display_name":"University of Washington Bothell","ror":"https://ror.org/02ygzhr13","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210138624"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Si","raw_affiliation_strings":["University of Washington Bothell, Bothell, WA, USA"],"affiliations":[{"raw_affiliation_string":"University of Washington Bothell, Bothell, WA, USA","institution_ids":["https://openalex.org/I4210138624"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037079603"],"corresponding_institution_ids":["https://openalex.org/I4210138624"],"apc_list":null,"apc_paid":null,"fwci":1.1799,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.87384316,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"691","last_page":"697"},"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":0.9998999834060669,"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":0.9998999834060669,"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/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9836999773979187,"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/resolution","display_name":"Resolution (logic)","score":0.7158620357513428},{"id":"https://openalex.org/keywords/trace","display_name":"TRACE (psycholinguistics)","score":0.6735694408416748},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4968447983264923},{"id":"https://openalex.org/keywords/electron-density","display_name":"Electron density","score":0.47498124837875366},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.4670238792896271},{"id":"https://openalex.org/keywords/low-resolution","display_name":"Low resolution","score":0.45519766211509705},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4059615135192871},{"id":"https://openalex.org/keywords/high-resolution","display_name":"High resolution","score":0.37438318133354187},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2992439866065979},{"id":"https://openalex.org/keywords/electron","display_name":"Electron","score":0.20049116015434265},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16471293568611145},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.09511864185333252},{"id":"https://openalex.org/keywords/remote-sensing","display_name":"Remote sensing","score":0.09318232536315918}],"concepts":[{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.7158620357513428},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.6735694408416748},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4968447983264923},{"id":"https://openalex.org/C125485243","wikidata":"https://www.wikidata.org/wiki/Q905186","display_name":"Electron density","level":3,"score":0.47498124837875366},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.4670238792896271},{"id":"https://openalex.org/C3019883945","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"Low resolution","level":3,"score":0.45519766211509705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4059615135192871},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.37438318133354187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2992439866065979},{"id":"https://openalex.org/C147120987","wikidata":"https://www.wikidata.org/wiki/Q2225","display_name":"Electron","level":2,"score":0.20049116015434265},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16471293568611145},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.09511864185333252},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.09318232536315918},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107501","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107501","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1558317748","https://openalex.org/W1995043996","https://openalex.org/W2053880783","https://openalex.org/W2084283552","https://openalex.org/W2152086886","https://openalex.org/W2169358216","https://openalex.org/W2568820001"],"related_works":["https://openalex.org/W4296995023","https://openalex.org/W2070173637","https://openalex.org/W3118545013","https://openalex.org/W2133155333","https://openalex.org/W1516116847","https://openalex.org/W2412281349","https://openalex.org/W4212954839","https://openalex.org/W4241811109","https://openalex.org/W4401570279","https://openalex.org/W3169440385"],"abstract_inverted_index":{"Cryo-electron":[0],"microscopy":[1],"(Cryo-EM)":[2],"is":[3,33,67,96,137,150],"able":[4,138],"to":[5,35,84,139],"achieve":[6],"high":[7,62],"resolution":[8,17,63,121],"density":[9,12,64,73,126,148],"maps.":[10,65],"These":[11],"maps":[13,118,127],"are":[14],"near":[15,155],"atomic":[16,156],"and":[18,42,55,78,90,106,122],"individual":[19],"atoms":[20,60],"can":[21],"be":[22],"seen":[23],"as":[24,26],"well":[25],"large":[27],"secondary":[28,81,108],"structure":[29,39,82,109],"elements.":[30],"However,":[31],"it":[32],"challenging":[34],"extract":[36],"the":[37,86,147],"backbone":[38,53,76,88,144],"information":[40],"automatically":[41],"efficiently.":[43],"This":[44],"paper":[45],"presents":[46],"a":[47,52,68,75,141],"novel":[48],"method":[49,71,95,114,136],"for":[50,61],"creating":[51],"trace":[54,77,89,145],"predicting":[56],"locations":[57],"of":[58,80],"C\u03b1":[59,91,143],"It":[66],"graph":[69],"based":[70],"utilizing":[72],"along":[74],"features":[79],"elements":[83],"find":[85],"optimal":[87],"atom":[92],"locations.":[93],"The":[94,131],"mostly":[97],"automatic":[98],"requiring":[99],"an":[100],"initial":[101],"user":[102],"determined":[103],"threshold":[104],"value":[105],"primary":[107],"type.":[110],"We":[111],"tested":[112],"our":[113,135],"on":[115],"fifteen":[116],"simulated":[117],"at":[119,154],"3A":[120],"four":[123],"experimental":[124],"cryo-EM":[125],"between":[128],"2.6-3.1A":[129],"resolution.":[130,157],"result":[132],"shows":[133],"that":[134],"generate":[140],"complete":[142],"when":[146],"map":[149],"not":[151],"missing":[152],"data":[153]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
