{"id":"https://openalex.org/W2169979181","doi":null,"title":"Protein sequence-structure alignment based on site-alignment probabilities.","display_name":"Protein sequence-structure alignment based on site-alignment probabilities.","publication_year":2000,"publication_date":"2000-01-01","ids":{"openalex":"https://openalex.org/W2169979181","mag":"2169979181","pmid":"https://pubmed.ncbi.nlm.nih.gov/11700595"},"language":"en","primary_location":{"id":"pmid:11700595","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11700595","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":"Genome informatics. Workshop on Genome Informatics","raw_type":"Journal Article"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":["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/A5073480262","display_name":"Sanzo Miyazawa","orcid":"https://orcid.org/0000-0002-5063-3661","observed_orcids":["https://orcid.org/0000-0002-5063-3661"]},"institutions":[{"id":"https://openalex.org/I165735259","display_name":"Gunma University","ror":"https://ror.org/046fm7598","country_code":"JP","type":"education","lineage":["https://openalex.org/I165735259"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"S Miyazawa","raw_affiliation_strings":["Faculty of Technology, Gunma University, Kiryu, Gunma 376, Japan. miyazawa@smlab.sci.gunma-u.ac.jp","Faculty of Technology, Gunma Univ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Technology, Gunma University, Kiryu, Gunma 376, Japan. miyazawa@smlab.sci.gunma-u.ac.jp","institution_ids":["https://openalex.org/I165735259"]},{"raw_affiliation_string":"Faculty of Technology, Gunma Univ","institution_ids":["https://openalex.org/I165735259"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073480262"],"corresponding_institution_ids":["https://openalex.org/I165735259"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"11","issue":null,"first_page":"141","last_page":"50"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.986299991607666,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.986299991607666,"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/T11162","display_name":"Enzyme Structure and Function","score":0.007199999876320362,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0008999999845400453,"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/mean-field-approximation","display_name":"mean-field approximation","score":0.6940000057220459},{"id":"https://openalex.org/keywords/gap-penalties","display_name":"gap penalties","score":0.6000000238418579},{"id":"https://openalex.org/keywords/low-sequence-identity","display_name":"low sequence identity","score":0.43299999833106995}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7832494974136353},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5884732604026794},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5878134965896606},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.541972815990448},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.4607497453689575},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.45986366271972656},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3351929485797882},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32642263174057007},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32254743576049805},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1914636194705963},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1576690673828125},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1520462930202484},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06545892357826233},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014534","descriptor_name":"UDPglucose 4-Epimerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014534","descriptor_name":"UDPglucose 4-Epimerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015067","descriptor_name":"17-Hydroxysteroid Dehydrogenases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015067","descriptor_name":"17-Hydroxysteroid Dehydrogenases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"pmid:11700595","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11700595","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":"Genome informatics. Workshop on Genome Informatics","raw_type":"Journal Article"},{"id":"mag:2169979181","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11700595","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W1547596077","https://openalex.org/W1589812083","https://openalex.org/W1759240213","https://openalex.org/W1965825291","https://openalex.org/W1975017420","https://openalex.org/W1994272924","https://openalex.org/W2008922464","https://openalex.org/W2011495938","https://openalex.org/W2014140912","https://openalex.org/W2016411902","https://openalex.org/W2027071679","https://openalex.org/W2027323314","https://openalex.org/W2031730136","https://openalex.org/W2033496784","https://openalex.org/W2035376403","https://openalex.org/W2038117444","https://openalex.org/W2040594319","https://openalex.org/W2040823078","https://openalex.org/W2041966417","https://openalex.org/W2047974333","https://openalex.org/W2060778016","https://openalex.org/W2071749306","https://openalex.org/W2085277871","https://openalex.org/W2104533281","https://openalex.org/W2136739161","https://openalex.org/W2139319441","https://openalex.org/W2143210482","https://openalex.org/W2161776897","https://openalex.org/W2171546617"],"related_works":["https://openalex.org/W2104533281","https://openalex.org/W1524556134","https://openalex.org/W2164308539","https://openalex.org/W2071749306","https://openalex.org/W2142801660","https://openalex.org/W7098471785","https://openalex.org/W146648400","https://openalex.org/W2275032899","https://openalex.org/W3100287249","https://openalex.org/W2129017214"],"abstract_inverted_index":{"A":[0],"protein":[1,107],"sequence-structure":[2,60,192],"alignment":[3,61,132,142],"method":[4,14,143,189],"for":[5,45,52],"database":[6],"searches":[7],"is":[8],"examined":[9],"on":[10,69,106],"how":[11],"effectively":[12],"this":[13,188],"together":[15],"with":[16,150,158],"a":[17,59,65,98,151,159],"simple":[18],"scoring":[19,33],"function":[20,34,140],"previously":[21],"developed":[22],"can":[23,144,171],"identify":[24],"compatibilities":[25],"between":[26],"sequences":[27,156],"and":[28,49,96,141,178],"structures":[29],"of":[30,36,43,72,74,90,165],"proteins.":[31],"The":[32],"consists":[35],"pairwise":[37,131],"contact":[38,56],"energies,":[39],"repulsive":[40],"packing":[41],"potentials":[42,51],"residues":[44],"overly":[46],"dense":[47],"arrangement":[48],"short-range":[50],"secondary":[53],"structures.":[54],"Pairwise":[55],"interactions":[57],"in":[58,64,110,128],"are":[62,82,194],"evaluated":[63],"mean":[66,175],"field":[67],"approximation":[68],"the":[70,88,137,184],"basis":[71],"probabilities":[73],"site":[75,126,168],"pairs":[76,127,169,182,193],"to":[77,84,87,114],"be":[78,85,102],"aligned.":[79],"Gap":[80],"penalties":[81],"assumed":[83],"proportional":[86],"number":[89],"contacts":[91],"at":[92],"each":[93],"residue":[94],"position,":[95],"as":[97],"result":[99],"gaps":[100],"will":[101],"more":[103],"frequently":[104],"placed":[105],"surfaces":[108],"than":[109],"cores.":[111],"In":[112],"addition":[113],"minimum":[115],"energy":[116,139],"alignments,":[117],"we":[118],"use":[119],"probability":[120],"alignments":[121,163],"made":[122],"by":[123,130,187],"successively":[124],"aligning":[125],"order":[129],"probabilities.":[133],"Results":[134],"show":[135],"that":[136],"present":[138],"detect":[145],"well":[146],"both":[147],"folds":[148],"compatible":[149,157],"given":[152,160],"sequence":[153,199],"and,":[154],"inversely,":[155],"fold.":[161],"Probability":[162],"consisting":[164],"most":[166],"reliable":[167,181],"only":[170,197],"yield":[172],"small":[173],"root":[174],"square":[176],"deviations,":[177],"including":[179],"less":[180],"increases":[183],"deviations.":[185],"Remarkably,":[186],"some":[190],"individual":[191],"detected":[195],"having":[196],"5-20%":[198],"identity.":[200]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}