{"id":"https://openalex.org/W2157809793","doi":"https://doi.org/10.1093/bioinformatics/bti828","title":"Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions","display_name":"Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions","publication_year":2005,"publication_date":"2005-12-13","ids":{"openalex":"https://openalex.org/W2157809793","doi":"https://doi.org/10.1093/bioinformatics/bti828","mag":"2157809793","pmid":"https://pubmed.ncbi.nlm.nih.gov/16352653"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti828","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti828","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/4/413/48840274/bioinformatics_22_4_413.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/4/413/48840274/bioinformatics_22_4_413.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027003060","display_name":"Yao-Ming Huang","orcid":"https://orcid.org/0000-0003-3583-3603"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yao-ming Huang","raw_affiliation_strings":["Center for Bioinformatics, Department of Biology, Rensselaer Polytechnic Institute \u00a0 Troy, NY 12180, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Biology, Rensselaer Polytechnic Institute \u00a0 Troy, NY 12180, USA","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105836918","display_name":"Christopher Bystroff","orcid":null},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher Bystroff","raw_affiliation_strings":["Center for Bioinformatics, Department of Biology, Rensselaer Polytechnic Institute \u00a0 Troy, NY 12180, USA"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Biology, Rensselaer Polytechnic Institute \u00a0 Troy, NY 12180, USA","institution_ids":["https://openalex.org/I165799507"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5105836918"],"corresponding_institution_ids":["https://openalex.org/I165799507"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7229,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.83624194,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"4","first_page":"413","last_page":"422"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9991000294685364,"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":0.9990000128746033,"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/structural-alignment","display_name":"Structural alignment","score":0.7149307727813721},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6688975691795349},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.6072860956192017},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5962028503417969},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5349375605583191},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5268577337265015},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5183326005935669},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5031594634056091},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.502417802810669},{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.49711039662361145},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4840099513530731},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.47659534215927124},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.4746304750442505},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.4700407385826111},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4596762955188751},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.45225974917411804},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.43488267064094543},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4253951907157898},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.41942548751831055},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4187256991863251},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2892765998840332},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2841486632823944},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2746993601322174},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2567151188850403},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16474848985671997},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08341595530509949}],"concepts":[{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.7149307727813721},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6688975691795349},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.6072860956192017},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5962028503417969},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5349375605583191},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5268577337265015},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5183326005935669},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5031594634056091},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.502417802810669},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.49711039662361145},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4840099513530731},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.47659534215927124},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.4746304750442505},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.4700407385826111},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4596762955188751},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.45225974917411804},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.43488267064094543},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4253951907157898},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.41942548751831055},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4187256991863251},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2892765998840332},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2841486632823944},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2746993601322174},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2567151188850403},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16474848985671997},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08341595530509949},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"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/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","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":"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":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti828","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti828","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/4/413/48840274/bioinformatics_22_4_413.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"},{"id":"pmid:16352653","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16352653","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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti828","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti828","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/4/413/48840274/bioinformatics_22_4_413.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":[{"display_name":"Reduced inequalities","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157809793.pdf","grobid_xml":"https://content.openalex.org/works/W2157809793.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W53898165","https://openalex.org/W1502621331","https://openalex.org/W1518942907","https://openalex.org/W1536270671","https://openalex.org/W1963866954","https://openalex.org/W1964795578","https://openalex.org/W1969621320","https://openalex.org/W1981448638","https://openalex.org/W1983265703","https://openalex.org/W2005313213","https://openalex.org/W2008841836","https://openalex.org/W2054849588","https://openalex.org/W2055043387","https://openalex.org/W2059754738","https://openalex.org/W2061033843","https://openalex.org/W2070265271","https://openalex.org/W2074774389","https://openalex.org/W2084136254","https://openalex.org/W2087064593","https://openalex.org/W2099075703","https://openalex.org/W2121272213","https://openalex.org/W2125838338","https://openalex.org/W2128328428","https://openalex.org/W2131724426","https://openalex.org/W2142383894","https://openalex.org/W2143210482","https://openalex.org/W2144472358","https://openalex.org/W2148311769","https://openalex.org/W2150627302","https://openalex.org/W2154889621","https://openalex.org/W2155658660","https://openalex.org/W2158714788","https://openalex.org/W2160672912","https://openalex.org/W2163860567","https://openalex.org/W2168211076","https://openalex.org/W2600349519","https://openalex.org/W4236236547","https://openalex.org/W4236356242","https://openalex.org/W4252684946","https://openalex.org/W6602161028","https://openalex.org/W6641385041","https://openalex.org/W6664387049","https://openalex.org/W6677959896"],"related_works":["https://openalex.org/W2111937814","https://openalex.org/W2501018882","https://openalex.org/W2166718648","https://openalex.org/W24291664","https://openalex.org/W2015399150","https://openalex.org/W2275032899","https://openalex.org/W2505756865","https://openalex.org/W2295731408","https://openalex.org/W2157930580","https://openalex.org/W2157809793"],"abstract_inverted_index":{"HMMSUM":[0,28,59,86],"(HMMSTR-based":[1],"substitution":[2,13,73],"matrices)":[3],"is":[4],"a":[5,17,24,49],"new":[6],"model":[7,52],"for":[8,23,53],"structural":[9],"context-based":[10],"amino":[11],"acid":[12],"probabilities":[14],"consisting":[15],"of":[16,19,34,42],"set":[18],"281":[20],"matrices,":[21],"each":[22],"different":[25],"sequence-structure":[26],"context.":[27],"does":[29],"not":[30],"require":[31],"the":[32,35,58,68,96],"structure":[33,44],"protein":[36],"to":[37,63],"be":[38],"known.":[39],"Instead,":[40],"predictions":[41],"local":[43,54,91],"are":[45],"made":[46],"using":[47,57,67,90],"HMMSTR,":[48],"hidden":[50],"Markov":[51],"structure.":[55],"Alignments":[56],"matrices":[60,70,74],"compare":[61],"favorably":[62],"alignments":[64,83],"carried":[65],"out":[66],"BLOSUM":[69],"or":[71],"structure-based":[72],"SDM":[75],"and":[76,94],"HSDM":[77],"when":[78],"validated":[79],"against":[80],"remote":[81],"homolog":[82],"from":[84],"BAliBASE.":[85],"has":[87],"been":[88],"implemented":[89],"Dynamic":[92],"Programming":[93],"with":[95],"Bayesian":[97],"Adaptive":[98],"alignment":[99],"method.":[100]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}
