{"id":"https://openalex.org/W3012316881","doi":"https://doi.org/10.1021/acs.jcim.9b01110","title":"MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry","display_name":"MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry","publication_year":2020,"publication_date":"2020-03-20","ids":{"openalex":"https://openalex.org/W3012316881","doi":"https://doi.org/10.1021/acs.jcim.9b01110","mag":"3012316881","pmid":"https://pubmed.ncbi.nlm.nih.gov/32197044"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01110","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01110","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9206428","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067994741","display_name":"Genki Terashi","orcid":"https://orcid.org/0000-0002-5339-909X"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Genki Terashi","raw_affiliation_strings":["Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008917271","display_name":"Yuki Kagaya","orcid":"https://orcid.org/0000-0003-0146-1709"},"institutions":[{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuki Kagaya","raw_affiliation_strings":["Graduate School of Information Sciences, Tohoku University, Aramaki Aza, Aoba 6-3-09, Aoba-Ku, Sendai, Miyagi 980-8579, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Sciences, Tohoku University, Aramaki Aza, Aoba 6-3-09, Aoba-Ku, Sendai, Miyagi 980-8579, Japan","institution_ids":["https://openalex.org/I201537933"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062293219","display_name":"Daisuke Kihara","orcid":"https://orcid.org/0000-0003-4091-6614"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daisuke Kihara","raw_affiliation_strings":["Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States","Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, United States","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062293219"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":null,"apc_paid":null,"fwci":0.8088,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.67186909,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"60","issue":"5","first_page":"2634","last_page":"2643"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9987000226974487,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9987000226974487,"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":0.9958999752998352,"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9950000047683716,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.7240684032440186},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6301596164703369},{"id":"https://openalex.org/keywords/cryo-electron-microscopy","display_name":"Cryo-electron microscopy","score":0.5937157869338989},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5918508768081665},{"id":"https://openalex.org/keywords/symmetry","display_name":"Symmetry (geometry)","score":0.5908606052398682},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5753864645957947},{"id":"https://openalex.org/keywords/salient","display_name":"Salient","score":0.5646042227745056},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45920661091804504},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4192489981651306},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4088713228702545},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.23961392045021057},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.23925873637199402},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1925765872001648},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14282819628715515}],"concepts":[{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.7240684032440186},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6301596164703369},{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.5937157869338989},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5918508768081665},{"id":"https://openalex.org/C2779886137","wikidata":"https://www.wikidata.org/wiki/Q21030012","display_name":"Symmetry (geometry)","level":2,"score":0.5908606052398682},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5753864645957947},{"id":"https://openalex.org/C2780719617","wikidata":"https://www.wikidata.org/wiki/Q1030752","display_name":"Salient","level":2,"score":0.5646042227745056},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45920661091804504},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4192489981651306},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4088713228702545},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.23961392045021057},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23925873637199402},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1925765872001648},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14282819628715515},{"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b01110","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01110","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32197044","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32197044","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9206428","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9206428","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9206428","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9206428","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5601722728","display_name":null,"funder_award_id":"CMMI1825941","funder_id":"https://openalex.org/F4320337391","funder_display_name":"Division of Civil, Mechanical and Manufacturing Innovation"},{"id":"https://openalex.org/G6027494520","display_name":null,"funder_award_id":"R01GM123055","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6310544451","display_name":null,"funder_award_id":"DMS1614777","funder_id":"https://openalex.org/F4320337380","funder_display_name":"Division of Mathematical Sciences"},{"id":"https://openalex.org/G7812654923","display_name":null,"funder_award_id":"MCB1925643","funder_id":"https://openalex.org/F4320337397","funder_display_name":"Division of Molecular and Cellular Biosciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"},{"id":"https://openalex.org/F4320337391","display_name":"Division of Civil, Mechanical and Manufacturing Innovation","ror":"https://ror.org/028yd4c30"},{"id":"https://openalex.org/F4320337397","display_name":"Division of Molecular and Cellular Biosciences","ror":"https://ror.org/002jdaq33"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1981372852","https://openalex.org/W2000630778","https://openalex.org/W2007107624","https://openalex.org/W2029314164","https://openalex.org/W2040646101","https://openalex.org/W2051567790","https://openalex.org/W2059274238","https://openalex.org/W2069920107","https://openalex.org/W2072973641","https://openalex.org/W2086549128","https://openalex.org/W2087492044","https://openalex.org/W2104130324","https://openalex.org/W2112035842","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2140831051","https://openalex.org/W2142748315","https://openalex.org/W2152764495","https://openalex.org/W2170693976","https://openalex.org/W2606766264","https://openalex.org/W2802061004","https://openalex.org/W2885035438","https://openalex.org/W2889917226","https://openalex.org/W2897504342","https://openalex.org/W2950686202","https://openalex.org/W2979414277","https://openalex.org/W4210352507"],"related_works":["https://openalex.org/W2329500892","https://openalex.org/W28991112","https://openalex.org/W2370726991","https://openalex.org/W2369710579","https://openalex.org/W4327728159","https://openalex.org/W4394266730","https://openalex.org/W1990856605","https://openalex.org/W2053783616","https://openalex.org/W2545348020","https://openalex.org/W2293263892"],"abstract_inverted_index":{"For":[0],"structural":[1],"interpretation":[2],"of":[3,27,33,60,82,113,130],"cryo-electron":[4],"microscopy":[5],"(cryo-EM)":[6],"density":[7,84,101,118],"maps":[8,53],"that":[9,78],"contain":[10],"multiple":[11],"chains,":[12],"map":[13,21,96],"segmentation":[14],"is":[15,22,57,148],"an":[16,41,58,123],"important":[17],"step.":[18],"If":[19],"a":[20,75,110],"segmented":[23],"accurately":[24],"into":[25],"regions":[26],"individual":[28,124],"protein":[29,35,66,72,125],"components,":[30],"the":[31,61,80,87,95,104,128,131],"structure":[32,67,77],"each":[34],"can":[36],"be":[37],"separately":[38],"modeled":[39],"using":[40],"existing":[42,141],"modeling":[43,68],"tool.":[44],"Here,":[45],"we":[46],"developed":[47],"new":[48],"software,":[49],"MAINMASTseg,":[50],"for":[51,127,152],"segmenting":[52],"with":[54],"symmetry.":[55],"MAINMASTseg":[56,89,108,120],"extension":[59],"MAINMAST":[62],"<i>de":[63],"novo</i>":[64],"cryo-EM":[65],"tool,":[69],"which":[70,133],"builds":[71],"structures":[73],"from":[74],"graph":[76,92],"captures":[79],"distribution":[81],"salient":[83],"points":[85,102],"in":[86,103],"map.":[88],"uses":[90],"this":[91],"and":[93,144],"segments":[94],"by":[97],"considering":[98],"symmetry":[99],"corresponding":[100],"graph.":[105],"We":[106],"tested":[107],"on":[109],"data":[111],"set":[112],"38":[114],"experimentally":[115],"determined":[116],"EM":[117],"maps.":[119],"successfully":[121],"identified":[122],"unit":[126],"majority":[129],"maps,":[132],"was":[134],"significantly":[135],"better":[136],"than":[137],"two":[138],"other":[139],"popular":[140],"methods,":[142],"Segger":[143],"Phenix.":[145],"The":[146],"software":[147],"made":[149],"freely":[150],"available":[151],"academic":[153],"users":[154],"at":[155],"http://kiharalab.org/mainmast_seg.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3}],"updated_date":"2026-03-03T08:47:05.690250","created_date":"2025-10-10T00:00:00"}
