{"id":"https://openalex.org/W1996904353","doi":"https://doi.org/10.1107/s0907444906023158","title":"Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach","display_name":"Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach","publication_year":2006,"publication_date":"2006-08-19","ids":{"openalex":"https://openalex.org/W1996904353","doi":"https://doi.org/10.1107/s0907444906023158","mag":"1996904353","pmid":"https://pubmed.ncbi.nlm.nih.gov/16929102"},"language":"en","primary_location":{"id":"doi:10.1107/s0907444906023158","doi":"https://doi.org/10.1107/s0907444906023158","is_oa":true,"landing_page_url":"https://doi.org/10.1107/s0907444906023158","pdf_url":"https://journals.iucr.org/d/issues/2006/09/00/wd5060/wd5060.pdf","source":{"id":"https://openalex.org/S114502960","display_name":"Acta Crystallographica Section D Biological Crystallography","issn_l":"0907-4449","issn":["0907-4449","1399-0047"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Acta Crystallographica Section D Biological Crystallography","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://journals.iucr.org/d/issues/2006/09/00/wd5060/wd5060.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040434303","display_name":"Reetal K. Pai","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reetal Pai","raw_affiliation_strings":["Department of Computer Science, Texas A and M University, TX, USA. reetalp@cs.tamu.edu","Department of Computer Science, Texas A&M University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A and M University, TX, USA. reetalp@cs.tamu.edu","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Computer Science, Texas A&M University, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103456216","display_name":"James C. Sacchettini","orcid":"https://orcid.org/0000-0001-5767-2367","observed_orcids":["https://orcid.org/0000-0001-5767-2367"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Sacchettini","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Texas A&amp;M University, USA","Department of Biochemistry and Biophysics, Texas A&M University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Texas A&amp;M University, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Texas A&M University, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048876954","display_name":"Thomas R. Ioerger","orcid":"https://orcid.org/0000-0001-8702-9102","observed_orcids":["https://orcid.org/0000-0001-8702-9102"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Ioerger","raw_affiliation_strings":["Department of Computer Science, Texas A&amp;M University, USA","Department of Computer Science, Texas A&M University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&amp;M University, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Computer Science, Texas A&M University, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":{"value":4740,"currency":"USD","value_usd":4740},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.12232707,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"62","issue":"9","first_page":"1012","last_page":"1021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9365000128746033,"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":0.9365000128746033,"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.05400000140070915,"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":0.005799999926239252,"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/non-crystallographic-symmetry","display_name":"non-crystallographic symmetry","score":1.0},{"id":"https://openalex.org/keywords/electron-density-maps","display_name":"electron density maps","score":0.8479999899864197},{"id":"https://openalex.org/keywords/rotation-invariant-features","display_name":"rotation-invariant features","score":0.9860000014305115},{"id":"https://openalex.org/keywords/brute-force-matching","display_name":"brute-force matching","score":0.8040000200271606},{"id":"https://openalex.org/keywords/protein-structure-determination","display_name":"protein structure determination","score":0.7099999785423279}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5122746825218201},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5069999694824219},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.5012826919555664},{"id":"https://openalex.org/C2779886137","wikidata":"https://www.wikidata.org/wiki/Q21030012","display_name":"Symmetry (geometry)","level":2,"score":0.4426797926425934},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43338608741760254},{"id":"https://openalex.org/C17020691","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operator (biology)","level":5,"score":0.41708552837371826},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3823168873786926},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36295729875564575},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3571866750717163},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.32043635845184326},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22845947742462158},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.1536710262298584},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11119970679283142},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D050543","descriptor_name":"Phosphoglycerate Dehydrogenase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1107/s0907444906023158","doi":"https://doi.org/10.1107/s0907444906023158","is_oa":true,"landing_page_url":"https://doi.org/10.1107/s0907444906023158","pdf_url":"https://journals.iucr.org/d/issues/2006/09/00/wd5060/wd5060.pdf","source":{"id":"https://openalex.org/S114502960","display_name":"Acta Crystallographica Section D Biological Crystallography","issn_l":"0907-4449","issn":["0907-4449","1399-0047"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Acta Crystallographica Section D Biological Crystallography","raw_type":"journal-article"},{"id":"pmid:16929102","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16929102","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,"listed_in":[],"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":"Acta crystallographica. Section D, Biological crystallography","raw_type":"Journal Article"},{"id":"pmh:oai:oaktrust.library.tamu.edu:1969.1/182720","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/1969.1/182720","pdf_url":null,"source":{"id":"https://openalex.org/S4306400291","display_name":"OakTrust (Texas A&M University Libraries)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I91045830","host_organization_name":"Texas A&M University","host_organization_lineage":["https://openalex.org/I91045830"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null}],"best_oa_location":{"id":"doi:10.1107/s0907444906023158","doi":"https://doi.org/10.1107/s0907444906023158","is_oa":true,"landing_page_url":"https://doi.org/10.1107/s0907444906023158","pdf_url":"https://journals.iucr.org/d/issues/2006/09/00/wd5060/wd5060.pdf","source":{"id":"https://openalex.org/S114502960","display_name":"Acta Crystallographica Section D Biological Crystallography","issn_l":"0907-4449","issn":["0907-4449","1399-0047"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Acta Crystallographica Section D Biological Crystallography","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1104986396","display_name":"Phenix: Integrated algorithms for high quality models from crystallographic and cryo-EM data","funder_award_id":"P01GM063210","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4442526607","display_name":null,"funder_award_id":"GM-63210","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1996904353.pdf","grobid_xml":"https://content.openalex.org/works/W1996904353.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W72107370","https://openalex.org/W285092801","https://openalex.org/W1517499021","https://openalex.org/W1581518593","https://openalex.org/W1937910784","https://openalex.org/W1970208847","https://openalex.org/W1977568127","https://openalex.org/W1984576926","https://openalex.org/W2024534366","https://openalex.org/W2027573930","https://openalex.org/W2031782903","https://openalex.org/W2047357501","https://openalex.org/W2065989745","https://openalex.org/W2076778009","https://openalex.org/W2080476827","https://openalex.org/W2084134149","https://openalex.org/W2091132606","https://openalex.org/W2093259914","https://openalex.org/W2108107014","https://openalex.org/W2126805362","https://openalex.org/W2128175348","https://openalex.org/W2135066023","https://openalex.org/W2140787958","https://openalex.org/W3017143921","https://openalex.org/W6680297068"],"related_works":["https://openalex.org/W2027573930","https://openalex.org/W2139289803","https://openalex.org/W3004383391","https://openalex.org/W2022470028","https://openalex.org/W1517499021","https://openalex.org/W2106425845","https://openalex.org/W2064093918","https://openalex.org/W2128831353","https://openalex.org/W6941316839","https://openalex.org/W2091116108"],"abstract_inverted_index":{"Non-crystallographic":[0],"symmetry":[1],"(NCS)":[2],"averaging":[3,178],"is":[4],"a":[5,75,143],"well":[6],"known":[7],"method":[8,70,123],"for":[9,158,187],"improving":[10],"the":[11,45,89,94,111,119,125,134,151,162,170],"quality":[12],"of":[13,24,48,127,146,161],"an":[14,180],"electron-density":[15,64],"map":[16,76,183],"and":[17,115,150,179],"thus":[18],"aiding":[19],"structure":[20],"determination.":[21],"Prior":[22],"methods":[23,57,138],"NCS-operator":[25],"determination":[26],"based":[27],"on":[28,142],"estimated":[29],"heavy-atom":[30],"positions":[31,126],"are":[32,66,102],"prone":[33],"to":[34,58,87,104,175],"errors":[35],"arising":[36],"from":[37,62],"inaccuracies":[38],"in":[39,44,74,182],"these":[40],"coordinates":[41],"or":[42,130],"differences":[43],"relative":[46],"orientations":[47],"domains":[49],"between":[50],"molecules.":[51],"In":[52],"this":[53],"paper,":[54],"two":[55],"real-space":[56],"determine":[59],"NCS":[60,153,166,177],"relationships":[61,154],"initial":[63],"maps":[65,149],"presented.":[67],"A":[68,81],"brute-force":[69,95,120],"identifies":[71],"matching":[72],"regions":[73,100],"by":[77,93,97,169],"local":[78],"density":[79,107],"correlation.":[80],"feature-based":[82,112,171],"algorithm":[83,96,113,172],"uses":[84],"rotation-invariant":[85],"features":[86],"reduce":[88],"computational":[90],"time":[91],"taken":[92],"filtering":[98],"out":[99],"that":[101],"likely":[103],"have":[105,139],"dissimilar":[106],"patterns.":[108],"This":[109],"makes":[110],"faster":[114],"as":[116,118],"accurate":[117],"approach.":[121],"Neither":[122],"requires":[124],"heavy":[128],"atoms":[129],"any":[131],"information":[132],"regarding":[133],"protein":[135],"sequence.":[136],"Both":[137],"been":[140],"tested":[141],"diverse":[144],"range":[145],"experimentally":[147],"phased":[148],"correct":[152],"were":[155,173],"accurately":[156],"identified":[157],"almost":[159],"all":[160],"test":[163],"cases.":[164,189],"The":[165],"operators":[167],"obtained":[168],"used":[174],"perform":[176],"improvement":[181],"correlation":[184],"was":[185],"observed":[186],"some":[188]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
