{"id":"https://openalex.org/W2112618708","doi":"https://doi.org/10.1142/s0219720004000594","title":"PREDICTION OF PROTEIN SECONDARY STRUCTURE BASED ON RESIDUE PAIRS","display_name":"PREDICTION OF PROTEIN SECONDARY STRUCTURE BASED ON RESIDUE PAIRS","publication_year":2004,"publication_date":"2004-05-27","ids":{"openalex":"https://openalex.org/W2112618708","doi":"https://doi.org/10.1142/s0219720004000594","mag":"2112618708","pmid":"https://pubmed.ncbi.nlm.nih.gov/15297986"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720004000594","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720004000594","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and 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/A5100352227","display_name":"Xin Liu","orcid":"https://orcid.org/0000-0002-4384-1876"},"institutions":[{"id":"https://openalex.org/I114218197","display_name":"Chinese Academy of Social Sciences","ror":"https://ror.org/05bxbmy32","country_code":"CN","type":"facility","lineage":["https://openalex.org/I114218197"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"XIN LIU","raw_affiliation_strings":["The Interdisciplinary Center of Theoretical Studies,  Chinese Academy of Sciences, Beijing 100080, China","The Interdisciplinary Center of Theoretical Studies, Chinese Academy of Sciences, Beijing 100080, China"],"affiliations":[{"raw_affiliation_string":"The Interdisciplinary Center of Theoretical Studies,  Chinese Academy of Sciences, Beijing 100080, China","institution_ids":["https://openalex.org/I114218197","https://openalex.org/I19820366"]},{"raw_affiliation_string":"The Interdisciplinary Center of Theoretical Studies, Chinese Academy of Sciences, Beijing 100080, China","institution_ids":["https://openalex.org/I114218197","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100415164","display_name":"Limei Zhang","orcid":"https://orcid.org/0000-0002-7383-8475"},"institutions":[{"id":"https://openalex.org/I21193070","display_name":"Beijing Jiaotong University","ror":"https://ror.org/01yj56c84","country_code":"CN","type":"education","lineage":["https://openalex.org/I21193070"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"LI-MEI ZHANG","raw_affiliation_strings":["School of Science at Beijing Jiaotong University, Beijing 100044, China"],"affiliations":[{"raw_affiliation_string":"School of Science at Beijing Jiaotong University, Beijing 100044, China","institution_ids":["https://openalex.org/I21193070"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021041719","display_name":"Wei\u2010Mou Zheng","orcid":"https://orcid.org/0000-0001-6546-2917"},"institutions":[{"id":"https://openalex.org/I4210125404","display_name":"Institute of Theoretical Physics","ror":"https://ror.org/02xtbq882","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210125404"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"WEI-MOU ZHENG","raw_affiliation_strings":["Institute of Theoretical Physics, China, Beijing 100080, China"],"affiliations":[{"raw_affiliation_string":"Institute of Theoretical Physics, China, Beijing 100080, China","institution_ids":["https://openalex.org/I4210125404"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100352227"],"corresponding_institution_ids":["https://openalex.org/I114218197","https://openalex.org/I19820366"],"apc_list":null,"apc_paid":null,"fwci":0.2339,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.53755139,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"02","issue":"02","first_page":"343","last_page":"352"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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/protein-secondary-structure","display_name":"Protein secondary structure","score":0.8178989887237549},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.5742889046669006},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5448094606399536},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.5391810536384583},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.4816288352012634},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4393089711666107},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.4357263743877411},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4229263365268707},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.381017804145813},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36313506960868835},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3370155692100525},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20655688643455505},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1450594961643219},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.12831050157546997}],"concepts":[{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.8178989887237549},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.5742889046669006},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5448094606399536},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.5391810536384583},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.4816288352012634},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4393089711666107},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.4357263743877411},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4229263365268707},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.381017804145813},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36313506960868835},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3370155692100525},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20655688643455505},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1450594961643219},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.12831050157546997},{"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":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"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":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":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:10.1142/s0219720004000594","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720004000594","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:15297986","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15297986","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1491040459","https://openalex.org/W1500658467","https://openalex.org/W1506812273","https://openalex.org/W1518016665","https://openalex.org/W1963550288","https://openalex.org/W1985818354","https://openalex.org/W1987037087","https://openalex.org/W2008708467","https://openalex.org/W2009664421","https://openalex.org/W2016339621","https://openalex.org/W2049695588","https://openalex.org/W2060234492","https://openalex.org/W2085277871","https://openalex.org/W2095450147","https://openalex.org/W2123838014","https://openalex.org/W2126871981","https://openalex.org/W2168211076","https://openalex.org/W2317912355","https://openalex.org/W2417106369","https://openalex.org/W4238603087"],"related_works":["https://openalex.org/W2731937419","https://openalex.org/W2045062364","https://openalex.org/W2017505838","https://openalex.org/W2728406523","https://openalex.org/W4206825711","https://openalex.org/W2928838901","https://openalex.org/W2155159626","https://openalex.org/W2494604670","https://openalex.org/W1578077690","https://openalex.org/W1998289425"],"abstract_inverted_index":{"The":[0],"GOR":[1],"program":[2,60,84],"for":[3,17,50,97],"predicting":[4,98],"protein":[5,67],"secondary":[6,68,99],"structure":[7,69],"is":[8,27,70,85],"extended":[9],"to":[10,21,53,65],"include":[11],"triple":[12],"correlation.":[13],"A":[14,59],"score":[15,63],"system":[16,64],"a":[18,42,77,92,104],"residue":[19],"pair":[20,46,52],"be":[22,54],"at":[23,38,55],"certain":[24],"conformation":[25],"state":[26],"derived":[28],"from":[29,81],"the":[30,45,48,51,56,74,83,101],"conditional":[31],"weight":[32],"matrix":[33],"describing":[34],"amino":[35],"acid":[36],"frequencies":[37],"each":[39],"position":[40],"of":[41],"window":[43],"flanking":[44],"under":[47],"condition":[49],"fixed":[57],"state.":[58],"using":[61,94],"this":[62],"predict":[66],"established.":[71],"After":[72],"training":[73],"model":[75],"with":[76,87],"learning":[78],"set":[79],"created":[80],"PDB_SELECT,":[82],"tested":[86],"two":[88],"test":[89],"sets.":[90],"As":[91],"method":[93],"single":[95],"sequence":[96],"structures,":[100],"approach":[102],"achieves":[103],"high":[105],"accuracy":[106],"near":[107],"70%.":[108]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}