{"id":"https://openalex.org/W2072631327","doi":"https://doi.org/10.1107/s0907444906002204","title":"A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure","display_name":"A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure","publication_year":2006,"publication_date":"2006-03-18","ids":{"openalex":"https://openalex.org/W2072631327","doi":"https://doi.org/10.1107/s0907444906002204","mag":"2072631327","pmid":"https://pubmed.ncbi.nlm.nih.gov/16552141","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2836325"},"language":"en","primary_location":{"id":"doi:10.1107/s0907444906002204","doi":"https://doi.org/10.1107/s0907444906002204","is_oa":false,"landing_page_url":"https://doi.org/10.1107/s0907444906002204","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2836325","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100887168","display_name":"Jay Il Jeong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I110273157","display_name":"Kookmin University","ror":"https://ror.org/0049erg63","country_code":"KR","type":"education","lineage":["https://openalex.org/I110273157"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jay I. Jeong","raw_affiliation_strings":["School of Mechanical and Automotive Engineering, Kookmin University Seoul 136702, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mechanical and Automotive Engineering, Kookmin University Seoul 136702, South Korea","institution_ids":["https://openalex.org/I110273157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036239205","display_name":"Eaton Edward Lattman","orcid":"https://orcid.org/0000-0002-7130-8964","observed_orcids":["https://orcid.org/0000-0002-7130-8964"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eaton E. Lattman","raw_affiliation_strings":["Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012775344","display_name":"Gregory S. Chirikjian","orcid":"https://orcid.org/0000-0003-0542-9028","observed_orcids":["https://orcid.org/0000-0003-0542-9028"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gregory S. Chirikjian","raw_affiliation_strings":["Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA","Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA#TAB#","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4740,"currency":"USD","value_usd":4740},"apc_paid":null,"fwci":1.0908,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.76327776,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"62","issue":"4","first_page":"398","last_page":"409"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9717000126838684,"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":0.9717000126838684,"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":0.027300000190734863,"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/T10464","display_name":"Crystal structures of chemical compounds","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-replacement","display_name":"molecular replacement","score":0.9900000095367432},{"id":"https://openalex.org/keywords/multidomain-proteins","display_name":"multidomain proteins","score":0.9909999966621399},{"id":"https://openalex.org/keywords/pose-estimation","display_name":"pose estimation","score":0.7300000190734863},{"id":"https://openalex.org/keywords/rotation-function","display_name":"rotation function","score":0.7390000224113464},{"id":"https://openalex.org/keywords/domain-orientation","display_name":"domain orientation","score":0.593999981880188},{"id":"https://openalex.org/keywords/ribose-binding-protein","display_name":"ribose-binding protein","score":0.9459999799728394},{"id":"https://openalex.org/keywords/lactoferrin","display_name":"lactoferrin","score":1.0},{"id":"https://openalex.org/keywords/ca2-atpase","display_name":"Ca2+-ATPase","score":0.9919999837875366}],"concepts":[{"id":"https://openalex.org/C74050887","wikidata":"https://www.wikidata.org/wiki/Q848368","display_name":"Rotation (mathematics)","level":2,"score":0.6261339783668518},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6161124110221863},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.596562385559082},{"id":"https://openalex.org/C2777166331","wikidata":"https://www.wikidata.org/wiki/Q17104122","display_name":"Molecular replacement","level":3,"score":0.5580911040306091},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5139390826225281},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.48108384013175964},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.468664288520813},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4552638828754425},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.4422774910926819},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.4374726116657257},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3980732262134552},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39438772201538086},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36450934410095215},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3322634696960449},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2628045082092285},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22589236497879028},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.19931575655937195},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1402258574962616},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.12270745635032654},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.10161501169204712},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.08826705813407898},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000252","descriptor_name":"Calcium-Transporting ATPases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004548","descriptor_name":"Elasticity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007781","descriptor_name":"Lactoferrin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011817","descriptor_name":"Rabbits","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012399","descriptor_name":"Rotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D033902","descriptor_name":"Periplasmic Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1107/s0907444906002204","doi":"https://doi.org/10.1107/s0907444906002204","is_oa":false,"landing_page_url":"https://doi.org/10.1107/s0907444906002204","pdf_url":null,"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:16552141","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16552141","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:pubmedcentral.nih.gov:2836325","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2836325","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Acta Crystallogr D Biol Crystallogr","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:2836325","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2836325","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Acta Crystallogr D Biol Crystallogr","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G4395783157","display_name":"Group-Theoretic Methods in Protein Structure Determina-n","funder_award_id":"R01GM075310","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1508596864","https://openalex.org/W1604172974","https://openalex.org/W1964573431","https://openalex.org/W1966379257","https://openalex.org/W1968407616","https://openalex.org/W1973481676","https://openalex.org/W2001449162","https://openalex.org/W2001930843","https://openalex.org/W2004067483","https://openalex.org/W2009073915","https://openalex.org/W2009745580","https://openalex.org/W2011890903","https://openalex.org/W2015280715","https://openalex.org/W2015642465","https://openalex.org/W2021419438","https://openalex.org/W2024464486","https://openalex.org/W2031340110","https://openalex.org/W2035638646","https://openalex.org/W2045101860","https://openalex.org/W2062809320","https://openalex.org/W2063962473","https://openalex.org/W2069777230","https://openalex.org/W2069920107","https://openalex.org/W2071152222","https://openalex.org/W2075409132","https://openalex.org/W2076089463","https://openalex.org/W2080476827","https://openalex.org/W2082462938","https://openalex.org/W2082841340","https://openalex.org/W2084631697","https://openalex.org/W2084763593","https://openalex.org/W2085277871","https://openalex.org/W2087340004","https://openalex.org/W2093151204","https://openalex.org/W2094218961","https://openalex.org/W2097493124","https://openalex.org/W2101017457","https://openalex.org/W2103856741","https://openalex.org/W2107007872","https://openalex.org/W2107076671","https://openalex.org/W2107557597","https://openalex.org/W2112315506","https://openalex.org/W2113994268","https://openalex.org/W2119097204","https://openalex.org/W2130479394","https://openalex.org/W2135066023","https://openalex.org/W2136995436","https://openalex.org/W2140889378","https://openalex.org/W2149301682","https://openalex.org/W2153331570","https://openalex.org/W2154733115","https://openalex.org/W2156115459","https://openalex.org/W2164069226","https://openalex.org/W2164548935"],"related_works":["https://openalex.org/W7095378298","https://openalex.org/W1969076643","https://openalex.org/W2001930843","https://openalex.org/W1969512615","https://openalex.org/W2007950357","https://openalex.org/W2083133427","https://openalex.org/W2024464486","https://openalex.org/W2329958849","https://openalex.org/W2132439237","https://openalex.org/W1990212322"],"abstract_inverted_index":{"This":[0,146],"paper":[1],"presents":[2,143],"a":[3,80,94,144,183],"methodology":[4],"to":[5,46,88,93,177,190],"obtain":[6],"candidate":[7,95,173,211,234],"conformations":[8,235],"of":[9,40,65,73,110,140,154,161,208,249],"multidomain":[10],"proteins":[11],"for":[12,104,236],"use":[13,237],"in":[14,54,122,131,213,238,253],"molecular":[15,35,239],"replacement.":[16,36],"For":[17],"each":[18,155,172,201],"separate":[19],"domain,":[20,156],"the":[21,25,28,41,48,52,55,63,71,77,90,99,105,111,118,123,137,141,158,168,185,204,209,214,221,228,244,250,254],"orientational":[22,38],"relationship":[23],"between":[24,51,76,164],"template":[26,91],"and":[27,67,166,197,206,241,247],"target":[29,56,106,251],"structure":[30,92],"is":[31,86,148,175,188],"obtained":[32,103,128],"using":[33,59],"standard":[34],"The":[37,108,224],"relationships":[39],"domains":[42,53,78,130],"are":[43,217],"then":[44],"used":[45,87],"calculate":[47],"relative":[49,74,162],"rotation":[50,75,124,163],"conformation":[57,96,174,212,252],"by":[58,150],"pose-estimation":[60],"techniques":[61],"from":[62,116,129,220],"field":[64],"robotics":[66],"computer":[68],"vision.":[69],"With":[70],"angle":[72],"as":[79],"cost":[81,169],"function,":[82],"iterative":[83,180],"normal-mode":[84],"analysis":[85],"drive":[89],"that":[97,227],"matches":[98],"X-ray":[100],"crystallographic":[101,255],"data":[102],"conformation.":[107],"selection":[109],"correct":[112],"intra-protein":[113],"domain":[114],"orientations":[115,127],"among":[117],"many":[119],"spurious":[120],"maxima":[121],"function":[125],"(including":[126],"symmetry":[132],"mates":[133],"rather":[134],"than":[135],"within":[136],"same":[138],"copy":[139],"protein)":[142],"challenge.":[145],"problem":[147],"resolved":[149],"checking":[151],"R":[152],"factors":[153],"measuring":[157],"absolute":[159],"value":[160,170],"domains,":[165],"evaluating":[167],"after":[171],"driven":[176],"convergence":[178],"with":[179],"NMA.":[181],"As":[182],"validation,":[184],"proposed":[186,229],"method":[187,230],"applied":[189],"three":[191],"test":[192,202],"proteins:":[193],"ribose-binding":[194],"protein,":[195],"lactoferrin":[196],"calcium":[198],"ATPase.":[199],"In":[200],"case,":[203],"orientation":[205],"translation":[207],"final":[210],"unit":[215,256],"cell":[216],"generated":[218],"correctly":[219],"suggested":[222],"procedure.":[223],"results":[225],"show":[226],"can":[231,242],"yield":[232],"viable":[233],"replacement":[240],"reveal":[243],"structural":[245],"details":[246],"pose":[248],"cell.":[257]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}