{"id":"https://openalex.org/W2108806594","doi":"https://doi.org/10.1186/1471-2105-9-94","title":"Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction","display_name":"Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction","publication_year":2008,"publication_date":"2008-02-11","ids":{"openalex":"https://openalex.org/W2108806594","doi":"https://doi.org/10.1186/1471-2105-9-94","mag":"2108806594","pmid":"https://pubmed.ncbi.nlm.nih.gov/18267018"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-94","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-94","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-94","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/10.1186/1471-2105-9-94","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015420457","display_name":"Ching-Wai Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ching-Wai Tan","raw_affiliation_strings":["Department of Computer Science, University College London, London, UK. chingwai@ntu.edu.sg","Dept. of Comput. Sci., Univ. Coll. London, London, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London, London, UK. chingwai@ntu.edu.sg","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Dept. of Comput. Sci., Univ. Coll. London, London, UK#TAB#","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068654082","display_name":"David T. Jones","orcid":"https://orcid.org/0000-0001-8626-3765"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"David T Jones","raw_affiliation_strings":["Department of Computer Science, University College London, London, UK","Dept. of Comput. Sci., Univ. Coll. London, London, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Dept. of Comput. Sci., Univ. Coll. London, London, UK#TAB#","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5068654082"],"corresponding_institution_ids":["https://openalex.org/I45129253"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.7798,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.71032793,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"9","issue":"1","first_page":"94","last_page":"94"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.41920000314712524,"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":0.41920000314712524,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.3474000096321106,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.07509999722242355,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/decoy","display_name":"Decoy","score":0.9870773553848267},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.7943567633628845},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7526546120643616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.632856011390686},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6194485425949097},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5254182815551758},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5105198621749878},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.4711274802684784},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4522547721862793},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35536953806877136},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14977237582206726},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07623991370201111}],"concepts":[{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.9870773553848267},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.7943567633628845},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7526546120643616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.632856011390686},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6194485425949097},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5254182815551758},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5105198621749878},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.4711274802684784},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4522547721862793},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35536953806877136},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14977237582206726},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07623991370201111},{"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/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":"D016002","descriptor_name":"Discriminant Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016002","descriptor_name":"Discriminant Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016002","descriptor_name":"Discriminant Analysis","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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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":"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":5,"locations":[{"id":"doi:10.1186/1471-2105-9-94","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-94","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-94","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:18267018","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18267018","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:doaj.org/article:e07f6e73de39487ebd62936177e13353","is_oa":false,"landing_page_url":"https://doaj.org/article/e07f6e73de39487ebd62936177e13353","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 94 (2008)","raw_type":"article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:103173","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/103173/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC BIOINFORMATICS , 9 , Article 94. (2008)","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2267779","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2267779","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-94","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-94","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-94","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":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6800000071525574}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320766","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108806594.pdf","grobid_xml":"https://content.openalex.org/works/W2108806594.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1497011462","https://openalex.org/W1589812083","https://openalex.org/W1640943318","https://openalex.org/W1992192767","https://openalex.org/W2008708467","https://openalex.org/W2013792107","https://openalex.org/W2023763252","https://openalex.org/W2030028095","https://openalex.org/W2040823078","https://openalex.org/W2042992947","https://openalex.org/W2047379058","https://openalex.org/W2047974333","https://openalex.org/W2050625197","https://openalex.org/W2052935924","https://openalex.org/W2052963427","https://openalex.org/W2085277871","https://openalex.org/W2105243761","https://openalex.org/W2110483430","https://openalex.org/W2117950175","https://openalex.org/W2121876872","https://openalex.org/W2131169717","https://openalex.org/W2142210548","https://openalex.org/W2143288492","https://openalex.org/W2145356476","https://openalex.org/W2147059525","https://openalex.org/W2149612698","https://openalex.org/W2150434184","https://openalex.org/W2153187042","https://openalex.org/W2154106236","https://openalex.org/W2157938277","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2161732286","https://openalex.org/W3201413583","https://openalex.org/W4256395558","https://openalex.org/W6603112357"],"related_works":["https://openalex.org/W2038772855","https://openalex.org/W2415073839","https://openalex.org/W1555596338","https://openalex.org/W1238053778","https://openalex.org/W2350944221","https://openalex.org/W4239355779","https://openalex.org/W2782845443","https://openalex.org/W2354605264","https://openalex.org/W2057946556","https://openalex.org/W2049700522"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1],"present":[2],"a":[3,25,43,150],"novel":[4],"method":[5,161],"of":[6,39,45,53,75,86,117,121,131,152],"protein":[7,40,55],"fold":[8],"decoy":[9,20,68,156,180],"discrimination":[10,21],"using":[11,16,42],"machine":[12,26],"learning,":[13],"more":[14],"specifically":[15],"neural":[17,30,97,107,135,176],"networks.":[18,98],"Here,":[19],"is":[22,109,137,162,171],"represented":[23],"as":[24,93],"learning":[27],"problem,":[28],"where":[29],"networks":[31,177],"are":[32,66,80],"used":[33,92,173],"to":[34,95,164,178],"learn":[35],"the":[36,58,73,83,96,104,110,127,132,138,146,175],"native-like":[37],"features":[38,79],"structures":[41,56,69],"set":[44,52,151],"positive":[46,59,87],"and":[47,88,91,126,167],"negative":[48,63,89],"training":[49,60,64,84],"examples.":[50],"A":[51],"native":[54,76,147],"provides":[57],"examples,":[61],"while":[62],"examples":[65,90],"simulated":[67],"obtained":[70],"by":[71],"reversing":[72],"sequences":[74],"structures.":[77],"Various":[78],"extracted":[81],"from":[82,149],"dataset":[85],"inputs":[94],"RESULTS:":[99],"Results":[100],"have":[101],"shown":[102],"that":[103,112],"best":[105,139],"performing":[106],"network":[108,136],"one":[111],"uses":[113],"input":[114],"information":[115,170],"comprising":[116],"PSI-BLAST":[118],"1":[119],"profiles":[120],"residue":[122],"pairs,":[123],"pairwise":[124],"distance":[125],"relative":[128],"solvent":[129],"accessibilities":[130],"residues.":[133],"This":[134,160],"among":[140],"all":[141,155],"methods":[142],"tested":[143],"in":[144,174],"discriminating":[145],"structure":[148],"decoys":[153],"for":[154],"datasets":[157],"tested.":[158],"CONCLUSION:":[159],"demonstrated":[163],"be":[165],"viable,":[166],"furthermore":[168],"evolutionary":[169],"successfully":[172],"improve":[179],"discrimination.":[181]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}