{"id":"https://openalex.org/W2125062378","doi":"https://doi.org/10.1093/bioinformatics/btm622","title":"A note on difficult structure alignment problems","display_name":"A note on difficult structure alignment problems","publication_year":2008,"publication_date":"2008-01-02","ids":{"openalex":"https://openalex.org/W2125062378","doi":"https://doi.org/10.1093/bioinformatics/btm622","mag":"2125062378","pmid":"https://pubmed.ncbi.nlm.nih.gov/18174182"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm622","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/426/50567960/bioinformatics_24_3_426.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/426/50567960/bioinformatics_24_3_426.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028301579","display_name":"Manfred J. Sippl","orcid":null},"institutions":[{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Manfred J. Sippl","raw_affiliation_strings":["Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria","institution_ids":["https://openalex.org/I182212641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073315136","display_name":"Markus Wiederstein","orcid":"https://orcid.org/0000-0002-4750-4746"},"institutions":[{"id":"https://openalex.org/I182212641","display_name":"University of Salzburg","ror":"https://ror.org/05gs8cd61","country_code":"AT","type":"education","lineage":["https://openalex.org/I182212641"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Markus Wiederstein","raw_affiliation_strings":["Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria","institution_ids":["https://openalex.org/I182212641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028301579"],"corresponding_institution_ids":["https://openalex.org/I182212641"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":8.3436,"has_fulltext":true,"cited_by_count":113,"citation_normalized_percentile":{"value":0.98543793,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"24","issue":"3","first_page":"426","last_page":"427"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9968000054359436,"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":0.6908854246139526},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6438125371932983},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.588370680809021},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.5151137709617615},{"id":"https://openalex.org/keywords/superposition-principle","display_name":"Superposition principle","score":0.5097338557243347},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.462363064289093},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45147600769996643},{"id":"https://openalex.org/keywords/structural-biology","display_name":"Structural biology","score":0.4239300489425659},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.39242780208587646},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3315998315811157},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23469552397727966},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19697263836860657},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09054058790206909},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07044932246208191}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6908854246139526},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6438125371932983},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.588370680809021},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.5151137709617615},{"id":"https://openalex.org/C27753989","wikidata":"https://www.wikidata.org/wiki/Q284885","display_name":"Superposition principle","level":2,"score":0.5097338557243347},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.462363064289093},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45147600769996643},{"id":"https://openalex.org/C191120209","wikidata":"https://www.wikidata.org/wiki/Q908902","display_name":"Structural biology","level":2,"score":0.4239300489425659},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.39242780208587646},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3315998315811157},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23469552397727966},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19697263836860657},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09054058790206909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07044932246208191},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D008969","descriptor_name":"Molecular Sequence Data","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":"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},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm622","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/426/50567960/bioinformatics_24_3_426.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18174182","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18174182","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm622","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm622","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/3/426/50567960/bioinformatics_24_3_426.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/W2125062378.pdf","grobid_xml":"https://content.openalex.org/works/W2125062378.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2011386686","https://openalex.org/W2041711253","https://openalex.org/W2056807348","https://openalex.org/W2128653811","https://openalex.org/W2130464038","https://openalex.org/W2130479394","https://openalex.org/W2132122858","https://openalex.org/W2136206199","https://openalex.org/W2137146016","https://openalex.org/W2144472358"],"related_works":["https://openalex.org/W2362470364","https://openalex.org/W4288061531","https://openalex.org/W2607853144","https://openalex.org/W1983338994","https://openalex.org/W3126783617","https://openalex.org/W3087805512","https://openalex.org/W2004353149","https://openalex.org/W2346580382","https://openalex.org/W2557251634","https://openalex.org/W2039737743"],"abstract_inverted_index":{"UNLABELLED:":[0],"Progress":[1],"in":[2,51],"structural":[3,44],"biology":[4],"depends":[5],"on":[6],"several":[7,56],"key":[8],"technologies.":[9],"In":[10],"particular":[11],"tools":[12],"for":[13,36,40,47],"alignment":[14],"and":[15,46],"superposition":[16],"of":[17,27,43],"protein":[18,37,52],"structures":[19],"are":[20],"indispensable.":[21],"Here":[22],"we":[23],"describe":[24],"the":[25,28,41],"use":[26],"TopMatch":[29,60],"web":[30,66],"service,":[31],"an":[32],"effective":[33],"computational":[34],"tool":[35],"structure":[38],"alignment,":[39],"visualization":[42],"similarities,":[45],"highlighting":[48],"relationships":[49],"found":[50],"classifications.":[53],"We":[54],"provide":[55],"instructive":[57],"examples.":[58],"AVAILABILITY:":[59],"is":[61],"available":[62],"as":[63],"a":[64],"public":[65],"service":[67],"at":[68],"http://services.came.sbg.ac.at.":[69]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":7},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":19}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
