{"id":"https://openalex.org/W1577593221","doi":"https://doi.org/10.1186/1471-2105-7-357","title":"Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps","display_name":"Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps","publication_year":2006,"publication_date":"2006-07-25","ids":{"openalex":"https://openalex.org/W1577593221","doi":"https://doi.org/10.1186/1471-2105-7-357","mag":"1577593221","pmid":"https://pubmed.ncbi.nlm.nih.gov/16869963"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-357","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-357","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-357","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/10.1186/1471-2105-7-357","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047414990","display_name":"Tomas Ohlson","orcid":null},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Tomas Ohlson","raw_affiliation_strings":["Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden. tomasoh@sbc.su.se","Stockholm Bioinformatics Center Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, SE-106 91 Stockholm, Sweden. tomasoh@sbc.su.se","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013751231","display_name":"Varun Aggarwal","orcid":"https://orcid.org/0000-0002-0442-5474"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["SE","US"],"is_corresponding":false,"raw_author_name":"Varun Aggarwal","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","Stockholm Bioinformatics Center, Stockholm University, SE-106 91, Stockholm, Sweden","Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, USA","Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, SE-106 91, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072903725","display_name":"Arne Elofsson","orcid":"https://orcid.org/0000-0002-7115-9751"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Arne Elofsson","raw_affiliation_strings":["Center for Biomembrane Research, Stockholm University, SE-106 91, Stockholm, Sweden","Stockholm Bioinformatics Center, Stockholm University, SE-106 91, Stockholm, Sweden","Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomembrane Research, Stockholm University, SE-106 91, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, SE-106 91, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090122303","display_name":"Robert M. MacCallum","orcid":"https://orcid.org/0000-0001-5070-4493"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB","SE"],"is_corresponding":false,"raw_author_name":"Robert M MacCallum","raw_affiliation_strings":["Division of Cell and Molecular Biology, Imperial College London, London, UK","Stockholm Bioinformatics Center, Stockholm University, SE-106 91, Stockholm, Sweden","Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Cell and Molecular Biology, Imperial College London, London, UK","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, SE-106 91, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]},{"raw_affiliation_string":"Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05903079,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"1","first_page":"357","last_page":"357"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7046999931335449,"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":0.7046999931335449,"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":0.11630000174045563,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.037300001829862595,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6806176900863647},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6242165565490723},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5700908303260803},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5516829490661621},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5487433671951294},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5412575006484985},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.528856098651886},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49430084228515625},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4738127291202545},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4442337155342102},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4356991648674011},{"id":"https://openalex.org/keywords/quality-score","display_name":"Quality Score","score":0.42648348212242126},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41691166162490845},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15000534057617188},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1419242024421692},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.0964595377445221},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09304165840148926},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08131143450737}],"concepts":[{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6806176900863647},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6242165565490723},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5700908303260803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5516829490661621},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5487433671951294},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5412575006484985},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.528856098651886},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49430084228515625},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4738127291202545},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4442337155342102},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4356991648674011},{"id":"https://openalex.org/C2779346075","wikidata":"https://www.wikidata.org/wiki/Q7268763","display_name":"Quality Score","level":3,"score":0.42648348212242126},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41691166162490845},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15000534057617188},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1419242024421692},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.0964595377445221},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09304165840148926},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08131143450737},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005544","descriptor_name":"Forecasting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005544","descriptor_name":"Forecasting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005544","descriptor_name":"Forecasting","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","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},{"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":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-7-357","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-357","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-357","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:16869963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16869963","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:dspace.mit.edu:1721.1/58739","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/58739","pdf_url":"http://hdl.handle.net/1721.1/58739","source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"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":"BioMed Central Ltd","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:europepmc.org:351604","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1562450","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1562450","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-357","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"},{"id":"mag:1577593221","is_oa":false,"landing_page_url":"http://dspace.mit.edu/handle/1721.1/58739","pdf_url":null,"source":{"id":"https://openalex.org/S4306504412","display_name":"BioMed Central Ltd","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"BioMed Central Ltd","raw_type":null}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-357","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-357","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-357","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":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1577593221.pdf","grobid_xml":"https://content.openalex.org/works/W1577593221.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1774262081","https://openalex.org/W1878410240","https://openalex.org/W1971751969","https://openalex.org/W1996357466","https://openalex.org/W2004228538","https://openalex.org/W2037960865","https://openalex.org/W2051969447","https://openalex.org/W2062296203","https://openalex.org/W2084466582","https://openalex.org/W2099075703","https://openalex.org/W2102677343","https://openalex.org/W2105801262","https://openalex.org/W2106241755","https://openalex.org/W2108138353","https://openalex.org/W2108212798","https://openalex.org/W2118836759","https://openalex.org/W2144483796","https://openalex.org/W2146983134","https://openalex.org/W2147667050","https://openalex.org/W2157809793","https://openalex.org/W2157938277","https://openalex.org/W2158714788","https://openalex.org/W2163822209","https://openalex.org/W2168508791","https://openalex.org/W2169097687","https://openalex.org/W4388297464"],"related_works":["https://openalex.org/W1708293692","https://openalex.org/W1723198065","https://openalex.org/W2020438176","https://openalex.org/W2091678889","https://openalex.org/W2169602699","https://openalex.org/W2415516439","https://openalex.org/W1866859902","https://openalex.org/W2014136705","https://openalex.org/W2155320525","https://openalex.org/W2015399150","https://openalex.org/W2547795274","https://openalex.org/W2183485040","https://openalex.org/W3114061096","https://openalex.org/W2098987612","https://openalex.org/W1971377345","https://openalex.org/W2144976187","https://openalex.org/W2137427011","https://openalex.org/W2112851850","https://openalex.org/W2144319229","https://openalex.org/W2577638289"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"sequence":[2,115,126],"alignment":[3,44,83,144,184],"is":[4,87,153,236],"one":[5],"of":[6,19,24,38,59,76,92,131,146,162,216],"the":[7,22,36,74,110,143,160,167,174,183,207,214,223,226,240],"basic":[8],"tools":[9],"in":[10,125,198],"bioinformatics.":[11],"Correct":[12],"alignments":[13,224],"are":[14],"required":[15],"for":[16],"a":[17,57,138,187],"range":[18],"tasks":[20],"including":[21],"derivation":[23],"phylogenetic":[25],"trees":[26],"and":[27,68,121],"protein":[28],"structure":[29,41,50,204],"prediction.":[30],"Numerous":[31],"studies":[32,200],"have":[33,52,211],"shown":[34,72,212],"that":[35,73,90,157,201,213,235],"incorporation":[37],"predicted":[39,163,202,241],"secondary":[40,164,203,242],"information":[42,168,234],"into":[43],"algorithms":[45],"improves":[46,142,206],"their":[47,123],"performance.":[48],"Secondary":[49],"predictors":[51],"to":[53,113,118,137,170,181,231],"be":[54,171,179],"trained":[55],"on":[56,82],"set":[58],"somewhat":[60],"arbitrarily":[61],"defined":[62],"states":[63,78],"(e.g.":[64],"helix,":[65],"strand,":[66],"coil),":[67],"it":[69,86],"has":[70,79,195],"been":[71,196],"choice":[75],"these":[77],"some":[80,233],"effect":[81],"quality.":[84],"However,":[85,166],"not":[88,237],"unlikely":[89],"prediction":[91,176],"other":[93],"structural":[94],"features":[95],"also":[96],"could":[97],"provide":[98],"an":[99,106],"improvement.":[100],"In":[101],"this":[102],"study":[103],"we":[104,210],"use":[105,124],"unsupervised":[107],"clustering":[108],"method,":[109],"self-organizing":[111,132,217,227],"map,":[112],"assign":[114],"profile":[116],"windows":[117],"\"structural":[119],"states\"":[120],"assess":[122],"alignment.":[127],"RESULTS:":[128],"The":[129,151],"addition":[130,215],"map":[133,218,228],"locations":[134,219,229],"as":[135,173,225],"inputs":[136],"profile-profile":[139],"scoring":[140],"function":[141],"quality":[145,185],"distantly":[147],"related":[148],"proteins":[149],"slightly.":[150],"improvement":[152],"slightly":[154],"smaller":[155],"than":[156],"gained":[158],"from":[159],"inclusion":[161],"structure.":[165,243],"seems":[169],"complementary":[172],"two":[175],"schemes":[177],"can":[178,220],"combined":[180],"improve":[182,222],"by":[186,239],"further":[188,221],"small":[189],"but":[190],"significant":[191],"amount.":[192],"CONCLUSION:":[193],"It":[194],"observed":[197],"many":[199],"significantly":[205],"alignments.":[208],"Here":[209],"seem":[230],"contain":[232],"captured":[238]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}