{"id":"https://openalex.org/W4206081925","doi":"https://doi.org/10.1186/s12859-021-04525-6","title":"Secondary structure specific simpler prediction models for protein backbone angles","display_name":"Secondary structure specific simpler prediction models for protein backbone angles","publication_year":2022,"publication_date":"2022-01-04","ids":{"openalex":"https://openalex.org/W4206081925","doi":"https://doi.org/10.1186/s12859-021-04525-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/34983370"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04525-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04525-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04525-6","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/s12859-021-04525-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086354302","display_name":"M. A. Hakim Newton","orcid":"https://orcid.org/0000-0001-5655-0683"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"M. A. Hakim Newton","raw_affiliation_strings":["Institute of Integrated and Intelligent Systems, Griffith University, Brisbane, Australia. mahakim.newton@griffith.edu.au","School of Information and Communication Technology, Griffith University, Brisbane, Australia. mahakim.newton@griffith.edu.au","Institute of Integrated and Intelligent Systems, Griffith University, Brisbane, Australia","School of Information and Communication Technology, Griffith University, Brisbane, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Integrated and Intelligent Systems, Griffith University, Brisbane, Australia. mahakim.newton@griffith.edu.au","institution_ids":[]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, Australia. mahakim.newton@griffith.edu.au","institution_ids":[]},{"raw_affiliation_string":"Institute of Integrated and Intelligent Systems, Griffith University, Brisbane, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037269180","display_name":"Fereshteh Mataeimoghadam","orcid":"https://orcid.org/0000-0002-7619-787X"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Fereshteh Mataeimoghadam","raw_affiliation_strings":["School of Information and Communication Technology, Griffith University, Brisbane, Australia. fereshteh.mataeimoghadam@griffithuni.edu.au","School of Information and Communication Technology, Griffith University, Brisbane, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, Australia. fereshteh.mataeimoghadam@griffithuni.edu.au","institution_ids":[]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091105936","display_name":"Rianon Zaman","orcid":"https://orcid.org/0000-0003-0763-5634"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Rianon Zaman","raw_affiliation_strings":["School of Information and Communication Technology, Griffith University, Brisbane, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038675407","display_name":"Abdul Sattar","orcid":"https://orcid.org/0000-0002-2567-2052"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Abdul Sattar","raw_affiliation_strings":["Institute of Integrated and Intelligent Systems, Griffith University, Brisbane, Australia","School of Information and Communication Technology, Griffith University, Brisbane, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Integrated and Intelligent Systems, Griffith University, Brisbane, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, Australia","institution_ids":["https://openalex.org/I11701301"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5037269180","https://openalex.org/A5086354302"],"corresponding_institution_ids":["https://openalex.org/I11701301"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6934,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65530342,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"23","issue":"1","first_page":"6","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8483999967575073,"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":0.8483999967575073,"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":0.061400000005960464,"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":0.055799998342990875,"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/protein-structure-prediction","display_name":"Protein structure prediction","score":0.6000359058380127},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5762250423431396},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5249614715576172},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47787585854530334},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4079291522502899},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33393433690071106},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31782108545303345},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23298195004463196},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10764613747596741},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08418643474578857}],"concepts":[{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.6000359058380127},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5762250423431396},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5249614715576172},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47787585854530334},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4079291522502899},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33393433690071106},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31782108545303345},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23298195004463196},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10764613747596741},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08418643474578857},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D016571","descriptor_name":"Neural Networks, Computer","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":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}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04525-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04525-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04525-6","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:34983370","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34983370","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:24059e088c7a458ba12fd15e20cd327a","is_oa":true,"landing_page_url":"https://doaj.org/article/24059e088c7a458ba12fd15e20cd327a","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-14 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8728911","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8728911","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":"pmh:oai:research-repository.griffith.edu.au:10072/411983","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/411983","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"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":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04525-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04525-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04525-6","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":"Quality Education","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4206081925.pdf","grobid_xml":"https://content.openalex.org/works/W4206081925.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W195150910","https://openalex.org/W1596947964","https://openalex.org/W1964655247","https://openalex.org/W1976005460","https://openalex.org/W2033767661","https://openalex.org/W2051210555","https://openalex.org/W2051872583","https://openalex.org/W2057289558","https://openalex.org/W2066507577","https://openalex.org/W2107024517","https://openalex.org/W2118387386","https://openalex.org/W2126729622","https://openalex.org/W2131474431","https://openalex.org/W2147209844","https://openalex.org/W2158714788","https://openalex.org/W2168337765","https://openalex.org/W2411998238","https://openalex.org/W2557595285","https://openalex.org/W2607268717","https://openalex.org/W2753650356","https://openalex.org/W2789241652","https://openalex.org/W2802316666","https://openalex.org/W2808950571","https://openalex.org/W2898320067","https://openalex.org/W2905446269","https://openalex.org/W2950374603","https://openalex.org/W2950865779","https://openalex.org/W2969644707","https://openalex.org/W2970105316","https://openalex.org/W3042567394","https://openalex.org/W3106449773","https://openalex.org/W6719385719"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W2043066834","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W1975122118","https://openalex.org/W1564749278","https://openalex.org/W2294851134"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"backbone":[2,130],"angle":[3],"prediction":[4,27],"has":[5],"achieved":[6],"significant":[7],"accuracy":[8],"improvement":[9],"with":[10,180],"the":[11,18,33,66,85,95,156,173],"development":[12],"of":[13,32,35,55,88,97,119,129,164],"deep":[14,20,49],"learning":[15,21,50,59],"methods.":[16],"Usually":[17],"same":[19],"model":[22],"is":[23,92,183],"used":[24],"in":[25,103,158],"making":[26],"for":[28,52,126,160],"all":[29,161],"residues":[30],"regardless":[31],"categories":[34],"secondary":[36,56],"structures":[37],"they":[38],"belong":[39],"to.":[40],"In":[41,73],"this":[42,74],"paper,":[43],"we":[44,76],"propose":[45],"to":[46,62,81,93,169,172],"train":[47],"separate":[48],"models":[51],"each":[53],"category":[54],"structures.":[57],"Machine":[58],"methods":[60,151],"strive":[61],"achieve":[63],"generality":[64],"over":[65],"training":[67,89],"examples":[68],"and":[69,123,141,154],"consequently":[70],"loose":[71],"accuracy.":[72],"work,":[75],"explicitly":[77],"exploit":[78],"classification":[79],"knowledge":[80,102],"restrict":[82],"generalisation":[83,98],"within":[84],"specific":[86],"class":[87],"examples.":[90],"This":[91],"compensate":[94],"loss":[96],"by":[99],"exploiting":[100],"specialisation":[101],"an":[104],"informed":[105],"way.":[106],"RESULTS:":[107],"The":[108],"new":[109],"method":[110],"named":[111],"SAP4SS":[112,146,178],"obtains":[113],"mean":[114],"absolute":[115],"error":[116],"(MAE)":[117],"values":[118],"15.59,":[120],"18.87,":[121],"6.03,":[122],"21.71":[124],"respectively":[125],"four":[127,162],"types":[128,163],"angles":[131,165],"[Formula:":[132,135,138,142],"see":[133,136,139,143],"text],":[134,137,140],"text].":[144],"Consequently,":[145],"significantly":[147],"outperforms":[148],"existing":[149],"state-of-the-art":[150],"SAP,":[152],"OPUS-TASS,":[153],"SPOT-1D:":[155],"differences":[157],"MAE":[159],"are":[166],"from":[167,185],"1.5":[168],"4.1%":[170],"compared":[171],"best":[174],"known":[175],"results.":[176],"AVAILABILITY:":[177],"along":[179],"its":[181],"data":[182],"available":[184],"https://gitlab.com/mahnewton/sap4ss":[186],".":[187]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}