{"id":"https://openalex.org/W1794629994","doi":"https://doi.org/10.1186/1471-2105-6-221","title":"GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures","display_name":"GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures","publication_year":2005,"publication_date":"2005-09-08","ids":{"openalex":"https://openalex.org/W1794629994","doi":"https://doi.org/10.1186/1471-2105-6-221","mag":"1794629994","pmid":"https://pubmed.ncbi.nlm.nih.gov/16146579"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-221","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-221","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-221","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-221","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003461562","display_name":"Daron M. Standley","orcid":"https://orcid.org/0000-0003-4078-0817"},"institutions":[{"id":"https://openalex.org/I4210152009","display_name":"Protein Research Foundation","ror":"https://ror.org/03yzv7g36","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210152009"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Daron M Standley","raw_affiliation_strings":["Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. standley@protein.osaka-u.ac.jp","Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. standley@protein.osaka-u.ac.jp","institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"]},{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106184369","display_name":"Hiroyuki Toh","orcid":null},"institutions":[{"id":"https://openalex.org/I135598925","display_name":"Kyushu University","ror":"https://ror.org/00p4k0j84","country_code":"JP","type":"education","lineage":["https://openalex.org/I135598925"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroyuki Toh","raw_affiliation_strings":["Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan","institution_ids":["https://openalex.org/I135598925"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035143113","display_name":"Haruki Nakamura","orcid":"https://orcid.org/0000-0001-6690-5863"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Haruki Nakamura","raw_affiliation_strings":["Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003461562"],"corresponding_institution_ids":["https://openalex.org/I4210152009","https://openalex.org/I98285908"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.0678,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.73405328,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"6","issue":"1","first_page":"221","last_page":"221"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8641999959945679,"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":0.8641999959945679,"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":0.10339999943971634,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.003700000001117587,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5577653050422668},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5113329291343689},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3561277985572815},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27106398344039917}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5577653050422668},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5113329291343689},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3561277985572815},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27106398344039917}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-6-221","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-221","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-221","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16146579","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16146579","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:catalog.lib.kyushu-u.ac.jp:2324/6018","is_oa":true,"landing_page_url":"http://hdl.handle.net/2324/6018","pdf_url":"http://hdl.handle.net/2324/6018","source":{"id":"https://openalex.org/S4306402148","display_name":"QIR (Kyushu University Institutional Repository) (Kyushu University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I135598925","host_organization_name":"Kyushu University","host_organization_lineage":["https://openalex.org/I135598925"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"journal article"},{"id":"pmh:oai:doaj.org/article:c8cfa211898b454f91178ca97c543192","is_oa":true,"landing_page_url":"https://doaj.org/article/c8cfa211898b454f91178ca97c543192","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 6, Iss 1, p 221 (2005)","raw_type":"article"},{"id":"pmh:oai:irdb.nii.ac.jp:01211:0005989292","is_oa":true,"landing_page_url":"https://hdl.handle.net/2324/6018","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1239909","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1239909","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-6-221","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-221","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-221","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1794629994.pdf","grobid_xml":"https://content.openalex.org/works/W1794629994.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W119935713","https://openalex.org/W160419203","https://openalex.org/W392215707","https://openalex.org/W1600463518","https://openalex.org/W1965910641","https://openalex.org/W1970614280","https://openalex.org/W1972718882","https://openalex.org/W1979147581","https://openalex.org/W1990258186","https://openalex.org/W1993971884","https://openalex.org/W2000629283","https://openalex.org/W2004589024","https://openalex.org/W2013025153","https://openalex.org/W2015292449","https://openalex.org/W2015608678","https://openalex.org/W2018927787","https://openalex.org/W2021566131","https://openalex.org/W2022058405","https://openalex.org/W2052928766","https://openalex.org/W2058844903","https://openalex.org/W2059790242","https://openalex.org/W2062296203","https://openalex.org/W2063639943","https://openalex.org/W2073953701","https://openalex.org/W2084443622","https://openalex.org/W2085277871","https://openalex.org/W2087064593","https://openalex.org/W2088347357","https://openalex.org/W2112422063","https://openalex.org/W2122300808","https://openalex.org/W2125083705","https://openalex.org/W2127054268","https://openalex.org/W2130479394","https://openalex.org/W2137146016","https://openalex.org/W2152326664","https://openalex.org/W2154882389","https://openalex.org/W2155479906","https://openalex.org/W2170120409","https://openalex.org/W4256395558","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,76],"introduce":[2],"GASH,":[3],"a":[4,24,90,102,229],"new,":[5],"publicly":[6],"accessible":[7],"program":[8,62,86,239],"for":[9,161,207,214],"structural":[10,28,36,165],"alignment":[11,37,113],"and":[12,65,82,138,151,194,203,228],"superposition.":[13],"Alignments":[14],"are":[15,41,58,126,167,240],"scored":[16],"by":[17,43,60,69,136,139,190],"the":[18,48,52,61,107,118,121,131,140,156,159,180,185,237],"Number":[19],"of":[20,27,47,95,112,120,124,130,142,173,198],"Equivalent":[21],"Residues":[22],"(NER),":[23],"quantitative":[25],"measure":[26],"similarity":[29],"that":[30],"can":[31,66],"be":[32,67],"applied":[33],"to":[34,79,83,155,178,236],"any":[35,72],"method.":[38],"Multiple":[39],"alignments":[40,57,70,125,160],"optimized":[42],"conjugate":[44],"gradient":[45],"maximization":[46],"NER":[49,137],"score":[50],"within":[51],"genetic":[53],"algorithm":[54],"framework.":[55],"Initial":[56],"generated":[59],"Local":[63],"ASH,":[64,193],"supplemented":[68],"from":[71,106],"other":[73],"program.":[74],"RESULTS:":[75],"compare":[77],"GASH":[78,183,204,221,238],"DaliLite,":[80,191],"CE,":[81],"our":[84],"earlier":[85],"Global":[87,192],"ASH":[88],"on":[89],"difficult":[91],"test":[92],"set":[93,104,123],"consisting":[94],"3,102":[96],"structure":[97],"pairs,":[98],"as":[99,101,115,117],"well":[100,116],"smaller":[103],"derived":[105],"Fischer-Eisenberg":[108],"set.":[109],"The":[110,128],"extent":[111],"crossover,":[114],"completeness":[119],"initial":[122],"examined.":[127],"quality":[129],"superpositions":[132],"is":[133,176,218],"evaluated":[134],"both":[135],"number":[141],"aligned":[143],"residues":[144],"under":[145,210],"three":[146],"different":[147],"RMSD":[148],"cutoffs":[149],"(2,4,":[150],"6A).":[152],"In":[153,196],"addition":[154],"numerical":[157],"assessment,":[158],"several":[162],"biologically":[163],"related":[164],"pairs":[166],"discussed":[168],"in":[169],"detail.":[170],"CONCLUSION:":[171],"Regardless":[172],"which":[174],"criteria":[175],"used":[177],"judge":[179],"superposition":[181],"accuracy,":[182],"achieves":[184],"best":[186],"overall":[187],"performance,":[188],"followed":[189],"CE.":[195,223],"terms":[197],"CPU":[199],"usage,":[200],"DaliLite":[201,217],"CE":[202],"perform":[205],"similarly":[206],"query":[208],"proteins":[209,216],"500":[211],"residues,":[212],"but":[213],"larger":[215],"faster":[219],"than":[220],"or":[222],"Both":[224],"an":[225],"http":[226],"interface":[227,235],"simple":[230],"object":[231],"application":[232],"protocol":[233],"(SOAP)":[234],"available":[241],"at":[242],"http://www.pdbj.org/GASH/.":[243]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}