{"id":"https://openalex.org/W2084482738","doi":"https://doi.org/10.1089/106652701300312896","title":"MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins","display_name":"MUSTA - A General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins","publication_year":2001,"publication_date":"2001-04-01","ids":{"openalex":"https://openalex.org/W2084482738","doi":"https://doi.org/10.1089/106652701300312896","mag":"2084482738","pmid":"https://pubmed.ncbi.nlm.nih.gov/11454300"},"language":"en","primary_location":{"id":"doi:10.1089/106652701300312896","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652701300312896","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","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/A5018484554","display_name":"Nathaniel Leibowitz","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Nathaniel Leibowitz","raw_affiliation_strings":["School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025357844","display_name":"Ruth Nussinov","orcid":"https://orcid.org/0000-0002-8115-6415"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ruth Nussinov","raw_affiliation_strings":["Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978,          Israel; Intramural Research Support Program-SAIC, Laboratory of Experimental and Computational Biology, NCI - FCRDC, Building 469, Room 151, Frederick, MD 21702"],"affiliations":[{"raw_affiliation_string":"Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978,          Israel; Intramural Research Support Program-SAIC, Laboratory of Experimental and Computational Biology, NCI - FCRDC, Building 469, Room 151, Frederick, MD 21702","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030975599","display_name":"Haim J. Wolfson","orcid":"https://orcid.org/0000-0002-7600-2702"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Haim J. Wolfson","raw_affiliation_strings":["School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5018484554"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":null,"apc_paid":null,"fwci":2.2576,"has_fulltext":false,"cited_by_count":68,"citation_normalized_percentile":{"value":0.88149324,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"2","first_page":"93","last_page":"121"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.998199999332428,"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":0.998199999332428,"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":0.9976999759674072,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9959999918937683,"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/computer-science","display_name":"Computer science","score":0.5791826248168945},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43143096566200256},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4193989932537079},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26429104804992676}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5791826248168945},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43143096566200256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4193989932537079},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26429104804992676}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005914","descriptor_name":"Globins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005914","descriptor_name":"Globins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005914","descriptor_name":"Globins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015843","descriptor_name":"Serpins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015843","descriptor_name":"Serpins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015843","descriptor_name":"Serpins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1089/106652701300312896","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652701300312896","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:11454300","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11454300","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1501400124","https://openalex.org/W1510161841","https://openalex.org/W1513073936","https://openalex.org/W1584136421","https://openalex.org/W1607669156","https://openalex.org/W1905708630","https://openalex.org/W1965907701","https://openalex.org/W1966041739","https://openalex.org/W1967762061","https://openalex.org/W1979147581","https://openalex.org/W1988625164","https://openalex.org/W1988874269","https://openalex.org/W1990061958","https://openalex.org/W1992558926","https://openalex.org/W1997379747","https://openalex.org/W2002921547","https://openalex.org/W2004178884","https://openalex.org/W2004470250","https://openalex.org/W2011495938","https://openalex.org/W2021211366","https://openalex.org/W2029198322","https://openalex.org/W2041318800","https://openalex.org/W2051256134","https://openalex.org/W2054729486","https://openalex.org/W2066603657","https://openalex.org/W2068154266","https://openalex.org/W2068282635","https://openalex.org/W2074231493","https://openalex.org/W2096943217","https://openalex.org/W2135338271","https://openalex.org/W2149385163","https://openalex.org/W2282054059","https://openalex.org/W2500928559","https://openalex.org/W2904250082","https://openalex.org/W4246356731","https://openalex.org/W4256395558","https://openalex.org/W4388250181"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"Here":[0],"we":[1,20],"present":[2],"an":[3],"algorithm":[4,114,148],"designed":[5,76],"to":[6,13,35,41,60,77,157],"carry":[7,78],"out":[8,79],"multiple":[9,91,99,111],"structure":[10,81,92,100,107],"alignment":[11,93,113,143],"and":[12,40,68,140],"detect":[14],"recurring":[15],"substructural":[16],"motifs.":[17],"So":[18],"far":[19],"have":[21,218],"implemented":[22],"it":[23],"for":[24],"comparison":[25,101,108],"of":[26,37,43,49,62,96,105,124,137,165,192,206,223,233],"protein":[27,65],"structures.":[28],"However,":[29],"this":[30],"general":[31],"method":[32,243],"is":[33,168,244],"applicable":[34],"comparisons":[36],"RNA":[38],"structures":[39],"detection":[42,61,136],"a":[44,47,86,103],"pharmacophore":[45],"in":[46,128,132,161,183,221],"series":[48],"drug":[50],"molecules.":[51,177],"Further,":[52],"its":[53,58],"sequence":[54],"order":[55],"independence":[56],"permits":[57],"application":[59],"motifs":[63],"on":[64],"surfaces,":[66],"interfaces,":[67],"binding/active":[69],"sites.":[70],"While":[71],"there":[72,83],"are":[73,84,144,155,174,181,213,228],"many":[74],"methods":[75],"pairwise":[80,106],"comparisons,":[82],"only":[85],"handful":[87],"geared":[88],"toward":[89],"the":[90,119,130,133,138,141,159,162,166,170,172,175,196,202,224,231,234,239],"task.":[94],"Most":[95],"these":[97],"tackle":[98],"as":[102],"collection":[104],"tasks.":[109],"The":[110,135,147,178,226,242],"structural":[112,142],"presented":[115],"here":[116],"automatically":[117],"finds":[118],"largest":[120],"common":[121,156],"substructure":[122],"(core)":[123],"atoms":[125,208],"that":[126,154,199,217],"appears":[127],"all":[129,158],"molecules":[131,167,198],"ensemble.":[134,163],"core":[139],"done":[145],"simultaneously.":[146],"begins":[149],"by":[150,237],"finding":[151],"small":[152,179,204,215],"substructures":[153,180,212,227],"proteins":[160],"One":[164],"considered":[169],"reference;":[171],"others":[173],"source":[176,197],"stored":[182],"special":[184],"arrays":[185],"termed":[186],"combinatorial":[187,235],"buckets,":[188,236],"which":[189],"define":[190],"sets":[191],"multistructural":[193],"alignments":[194],"from":[195],"coincide":[200],"with":[201],"same":[203],"set":[205],"reference":[207],"(C(alpha)-atoms":[209],"here).":[210],"These":[211],"initial":[214],"fragments":[216],"congruent":[219],"copies":[220],"each":[222],"proteins.":[225],"extended,":[229],"through":[230],"processing":[232],"clustering":[238],"superpositions":[240],"(transformations).":[241],"very":[245],"efficient.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}