{"id":"https://openalex.org/W2103486885","doi":"https://doi.org/10.1093/bioinformatics/btp251","title":"MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields","display_name":"MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields","publication_year":2009,"publication_date":"2009-04-09","ids":{"openalex":"https://openalex.org/W2103486885","doi":"https://doi.org/10.1093/bioinformatics/btp251","mag":"2103486885"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp251","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp251","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1433/48989809/bioinformatics_25_11_1433.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1433/48989809/bioinformatics_25_11_1433.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032548061","display_name":"Xuefeng Xia","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xuefeng Xia","raw_affiliation_strings":["Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100366512","display_name":"Song Zhang","orcid":"https://orcid.org/0000-0001-6685-8673"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Song Zhang","raw_affiliation_strings":["Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108481279","display_name":"Yu Su","orcid":"https://orcid.org/0000-0003-0685-2768"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Su","raw_affiliation_strings":["Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054065249","display_name":"Zhirong Sun","orcid":"https://orcid.org/0000-0003-4819-8223"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhirong Sun","raw_affiliation_strings":["Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032548061"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2625,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.59323581,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"25","issue":"11","first_page":"1433","last_page":"1434"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9745000004768372,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9362999796867371,"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/sequence","display_name":"Sequence (biology)","score":0.7093361616134644},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.7030760049819946},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.631024956703186},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4401301443576813},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.400442510843277},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3642866909503937},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3305972218513489},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0705353319644928},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.06457030773162842},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06351742148399353}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7093361616134644},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.7030760049819946},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.631024956703186},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4401301443576813},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.400442510843277},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3642866909503937},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3305972218513489},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0705353319644928},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.06457030773162842},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06351742148399353},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btp251","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp251","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1433/48989809/bioinformatics_25_11_1433.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp251","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp251","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/11/1433/48989809/bioinformatics_25_11_1433.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103486885.pdf","grobid_xml":"https://content.openalex.org/works/W2103486885.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1489075871","https://openalex.org/W1978304263","https://openalex.org/W1982505048","https://openalex.org/W2004228538","https://openalex.org/W2045103836","https://openalex.org/W2101220662","https://openalex.org/W2105840826","https://openalex.org/W2106882534","https://openalex.org/W2108642468","https://openalex.org/W2121702291","https://openalex.org/W2127122014","https://openalex.org/W2143292980","https://openalex.org/W2144357990","https://openalex.org/W2147880316","https://openalex.org/W2149758239","https://openalex.org/W2151904894","https://openalex.org/W2161738189","https://openalex.org/W6682082992"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2141411672"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"Sequence-to-structure":[2],"alignment":[3,29,88,94],"in":[4],"template-based":[5],"protein":[6],"structure":[7],"modeling":[8],"for":[9,108],"remote":[10],"homologs":[11],"remains":[12],"a":[13,27,67],"difficult":[14],"problem":[15],"even":[16],"following":[17],"the":[18,79],"correct":[19],"recognition":[20],"of":[21,35,41],"folds.":[22],"Here":[23],"we":[24],"present":[25],"MICAlign,":[26],"sequence-to-structure":[28],"tool":[30],"that":[31],"incorporates":[32],"multiple":[33],"sources":[34],"information":[36],"from":[37],"local":[38],"structural":[39],"contexts":[40],"template,":[42],"sequence":[43],"profiles,":[44],"predicted":[45],"secondary":[46],"structures,":[47],"solvent":[48,56],"accessibilities,":[49],"potential-like":[50],"terms":[51],"(including":[52],"residue\u2013residue":[53],"contacts":[54],"and":[55,58,61,112],"exposures)":[57],"pre-aligned":[59],"structures":[60],"sequences.":[62],"These":[63],"features,":[64],"together":[65],"with":[66],"position-specific":[68],"gap":[69],"scheme,":[70],"were":[71,82],"integrated":[72],"into":[73],"conditional":[74],"random":[75],"fields":[76],"through":[77],"which":[78],"optimal":[80],"parameters":[81],"automatically":[83],"learned.":[84],"MICAlign":[85],"showed":[86],"improved":[87],"accuracy":[89],"over":[90],"several":[91],"other":[92],"state-of-the-art":[93],"tools":[95],"based":[96],"on":[97],"comparisons":[98],"by":[99],"using":[100],"independent":[101],"datasets.":[102],"Availability:":[103],"Freely":[104],"available":[105,122],"at":[106,123],"http://www.bioinfo.tsinghua.edu.cn/\u223cxiaxf/micalign":[107],"both":[109],"web":[110],"server":[111],"source":[113],"code.":[114],"Contact:":[115],"sunzhr@mail.tsinghua.edu.cn":[116],"Supplementary":[117,119],"information:":[118],"data":[120],"are":[121],"Bioinformatics":[124],"online.":[125]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
