{"id":"https://openalex.org/W2117440917","doi":"https://doi.org/10.1109/csb.2004.1332439","title":"Weighting features to recognize 3D patterns of electron density in x-ray protein crystallography","display_name":"Weighting features to recognize 3D patterns of electron density in x-ray protein crystallography","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W2117440917","doi":"https://doi.org/10.1109/csb.2004.1332439","mag":"2117440917","pmid":"https://pubmed.ncbi.nlm.nih.gov/16448019"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332439","doi":"https://doi.org/10.1109/csb.2004.1332439","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332439","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"IEEE Computational Systems Bioinformatics Conference (CSB)","issn_l":"1752-7791","issn":["1752-7791"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":["jufo-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref","pubmed"],"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/A5113736935","display_name":"K. Gopal","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":"K. Gopal","raw_affiliation_strings":["Department of Computer Science, Texas A&M University, USA. kgopal@cs.tamu.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A&M University, USA. kgopal@cs.tamu.edu","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063213982","display_name":"T.D. Romo","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":"T.D. Romo","raw_affiliation_strings":["Department of Biochemistry & Biophysics, Texas A and M University, USA","Texas A&M University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, Texas A and M University, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Texas A&M University","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":"J.C. Sacchettini","raw_affiliation_strings":["Department of Biochemistry & Biophysics, Texas A and M University, USA","Texas A&M University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, Texas A and M University, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Texas A&M University","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":"T.R. Ioerger","raw_affiliation_strings":["Department of Computer Science, Texas A and M University, USA","Texas A&M University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Texas A and M University, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Texas A&M University","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":null,"apc_paid":null,"fwci":2.7031,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.89342524,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"d5","issue":null,"first_page":"246","last_page":"256"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.8417999744415283,"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":0.8417999744415283,"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":0.07190000265836716,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.019600000232458115,"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/feature-weighting","display_name":"feature weighting","score":0.9070000052452087},{"id":"https://openalex.org/keywords/feature-selection","display_name":"feature selection","score":0.953000009059906},{"id":"https://openalex.org/keywords/protein-structure-determination","display_name":"protein structure determination","score":0.8669999837875366},{"id":"https://openalex.org/keywords/x-ray-crystallography","display_name":"X-ray crystallography","score":0.753000020980835},{"id":"https://openalex.org/keywords/instance-based-learning","display_name":"instance-based learning","score":0.7279999852180481},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"nearest neighbor search","score":0.675000011920929},{"id":"https://openalex.org/keywords/distance-metrics","display_name":"distance measures","score":0.6840000152587891},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"pattern recognition","score":0.42399999499320984}],"concepts":[{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.9051222801208496},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6732637882232666},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6631518602371216},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.6597107648849487},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6056628227233887},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5121819972991943},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.4745543599128723},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.4732266664505005},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.4606606364250183},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45235732197761536},{"id":"https://openalex.org/C198043062","wikidata":"https://www.wikidata.org/wiki/Q180953","display_name":"Metric space","level":2,"score":0.43903791904449463},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.41097119450569153},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3727818727493286},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3585083484649658},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11820802092552185},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10369858145713806},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","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":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015502","descriptor_name":"Absorptiometry, Photon","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/csb.2004.1332439","doi":"https://doi.org/10.1109/csb.2004.1332439","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332439","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"IEEE Computational Systems Bioinformatics Conference (CSB)","issn_l":"1752-7791","issn":["1752-7791"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":["jufo-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},{"id":"pmid:16448019","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16448019","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":"Proceedings. IEEE Computational Systems Bioinformatics Conference","raw_type":"Journal Article"},{"id":"mag:2117440917","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16448019","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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W73774838","https://openalex.org/W117742025","https://openalex.org/W213113363","https://openalex.org/W1487906362","https://openalex.org/W1497078786","https://openalex.org/W1500151553","https://openalex.org/W1522207166","https://openalex.org/W1534519688","https://openalex.org/W1581518593","https://openalex.org/W1583700199","https://openalex.org/W1593454066","https://openalex.org/W1619226191","https://openalex.org/W1967320885","https://openalex.org/W1989344766","https://openalex.org/W2010352922","https://openalex.org/W2040884411","https://openalex.org/W2087064593","https://openalex.org/W2088774638","https://openalex.org/W2096581064","https://openalex.org/W2098504064","https://openalex.org/W2122410182","https://openalex.org/W2128304800","https://openalex.org/W2130479394","https://openalex.org/W2136503847","https://openalex.org/W2137995988","https://openalex.org/W2142243947","https://openalex.org/W2145679404","https://openalex.org/W2146142293","https://openalex.org/W2150687797","https://openalex.org/W2170585418","https://openalex.org/W2193474915","https://openalex.org/W2504658994","https://openalex.org/W2799061466","https://openalex.org/W2911640577","https://openalex.org/W3141271909","https://openalex.org/W4285719527","https://openalex.org/W7100074115"],"related_works":["https://openalex.org/W7095677564","https://openalex.org/W2024297195","https://openalex.org/W2524759236","https://openalex.org/W1522207166","https://openalex.org/W2114009629","https://openalex.org/W2134551000","https://openalex.org/W2009002107","https://openalex.org/W2170585418","https://openalex.org/W2083812665","https://openalex.org/W1996260281"],"abstract_inverted_index":{"Feature":[0],"selection":[1],"and":[2,10,22,80],"weighting":[3,23],"are":[4,53],"central":[5],"problems":[6],"in":[7,70,116],"pattern":[8],"recognition":[9],"instance-based":[11],"learning.":[12],"In":[13],"this":[14],"work,":[15],"we":[16],"discuss":[17],"the":[18,93,103,117,125,132,146],"challenges":[19],"of":[20,29,64,95,119],"constructing":[21],"features":[24],"to":[25,32,67,87,98,131,140,145,150],"recognize":[26],"3D":[27],"patterns":[28,48,82],"electron":[30,121],"density":[31,122],"determine":[33],"protein":[34],"structures.":[35],"We":[36,101],"present":[37],"SLIDER,":[38],"a":[39,141],"feature-weighting":[40],"algorithm":[41],"that":[42,47,49,113],"adjusts":[43],"weights":[44,76,112],"iteratively":[45],"such":[46],"match":[50],"query":[51,88],"instances":[52],"better":[54],"ranked":[55],"than":[56],"mismatching":[57,81],"ones.":[58],"Moreover,":[59],"SLIDER":[60,109],"makes":[61],"judicious":[62],"choices":[63],"weight":[65,96,127],"values":[66],"be":[68,99],"considered":[69],"each":[71],"iteration,":[72],"by":[73],"examining":[74],"specific":[75],"at":[77],"which":[78],"matching":[79,120],"switch":[83],"as":[84],"nearest":[85],"neighbors":[86],"instances.":[89],"This":[90],"approach":[91],"reduces":[92],"space":[94],"vectors":[97],"searched.":[100],"make":[102],"following":[104],"two":[105],"main":[106],"observations:":[107],"(1)":[108],"efficiently":[110],"generates":[111],"contribute":[114],"significantly":[115],"retrieval":[118],"patterns;":[123],"(2)":[124],"optimum":[126],"vector":[128],"is":[129],"sensitive":[130,144],"distance":[133],"metric":[134,148],"i.e.":[135],"feature":[136],"relevance":[137],"can":[138],"be,":[139],"certain":[142],"extent,":[143],"underlying":[147],"used":[149],"compare":[151],"patterns.":[152]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
