{"id":"https://openalex.org/W2749729134","doi":"https://doi.org/10.1145/3107411.3107500","title":"Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool","display_name":"Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2749729134","doi":"https://doi.org/10.1145/3107411.3107500","mag":"2749729134"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107500","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107500","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/A5059284872","display_name":"Michael Nissenson","orcid":null},"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":"Michael Nissenson","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/A5059284872"],"corresponding_institution_ids":["https://openalex.org/I4210138624"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07842182,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"685","last_page":"690"},"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/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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.993399977684021,"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/volume","display_name":"Volume (thermodynamics)","score":0.7560365200042725},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7390127778053284},{"id":"https://openalex.org/keywords/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.7316304445266724},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5632690787315369},{"id":"https://openalex.org/keywords/macro","display_name":"Macro","score":0.4514252245426178},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37808430194854736},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33260905742645264}],"concepts":[{"id":"https://openalex.org/C20556612","wikidata":"https://www.wikidata.org/wiki/Q4469374","display_name":"Volume (thermodynamics)","level":2,"score":0.7560365200042725},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7390127778053284},{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.7316304445266724},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5632690787315369},{"id":"https://openalex.org/C166955791","wikidata":"https://www.wikidata.org/wiki/Q629579","display_name":"Macro","level":2,"score":0.4514252245426178},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37808430194854736},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33260905742645264},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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},{"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107500","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107500","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":[{"id":"https://openalex.org/F4320334502","display_name":"University of Washington Bothell","ror":"https://ror.org/02ygzhr13"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W173687888","https://openalex.org/W1966323820","https://openalex.org/W1982295411","https://openalex.org/W1995043996","https://openalex.org/W1998997744","https://openalex.org/W2020337704","https://openalex.org/W2053880783","https://openalex.org/W2070524991","https://openalex.org/W2075824676","https://openalex.org/W2091096627","https://openalex.org/W2104234755","https://openalex.org/W2132629607","https://openalex.org/W2133442602","https://openalex.org/W2152086886","https://openalex.org/W2164659462","https://openalex.org/W2168310604","https://openalex.org/W2169799657","https://openalex.org/W2209329607","https://openalex.org/W2576361275","https://openalex.org/W2614431492"],"related_works":["https://openalex.org/W2030816003","https://openalex.org/W4239992647","https://openalex.org/W2150013480","https://openalex.org/W1554458299","https://openalex.org/W81423522","https://openalex.org/W1509860481","https://openalex.org/W2488264085","https://openalex.org/W2076325756","https://openalex.org/W4386206750","https://openalex.org/W4238700786"],"abstract_inverted_index":{"In":[0],"electron":[1],"cryo-microscopy":[2],"(cryo-EM),":[3],"manual":[4],"isolation":[5],"of":[6,76,89,108,131,137],"volumetric":[7,42],"protein":[8,14,46,90],"density":[9,97],"map":[10],"data":[11,43,65,68,100,121,124,133],"surrounding":[12,44],"known":[13],"structures":[15],"is":[16],"a":[17,31],"time-consuming":[18],"process":[19],"that":[20,53,115],"requires":[21],"constant":[22],"expert":[23],"attention":[24],"for":[25,86,134,141],"multiple":[26],"hours.":[27],"This":[28,58],"paper":[29],"presents":[30],"tool,":[32],"Volume":[33],"Cut,":[34],"and":[35,67,102],"an":[36,106,126],"algorithm":[37],"to":[38,71,128],"automatically":[39],"isolate":[40],"the":[41,49,64,87,117,135],"individual":[45],"chains":[47],"from":[48,93],"entire":[50],"macro-molecular":[51],"complex":[52],"runs":[54],"in":[55,63,113,125],"just":[56],"minutes.":[57],"tool":[59,110],"can":[60,82,144],"be":[61,83,145],"used":[62,85],"collection":[66],"pre-processing":[69],"steps":[70],"generate":[72],"good":[73],"training":[74],"datasets":[75],"single":[77],"chain":[78],"volume-structure":[79],"pairs,":[80],"which":[81],"further":[84],"study":[88],"structure":[91],"prediction":[92],"experimental":[94,119,132],"3D":[95],"cryo-EM":[96,120],"maps":[98],"using":[99],"mining":[101],"machine":[103],"learning.":[104],"Additionally,":[105],"application":[107],"this":[109],"was":[111],"explored":[112],"depth":[114],"compares":[116],"cut":[118],"with":[122],"simulated":[123],"attempt":[127],"find":[129],"irregularities":[130],"purpose":[136],"validation.":[138],"The":[139],"source":[140],"both":[142],"tools":[143],"found":[146],"at":[147],"https://github.com/nissensonm/VolumeCut/.":[148]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}