{"id":"https://openalex.org/W3093108887","doi":"https://doi.org/10.1002/jcc.26432","title":"ProteinUnet\u2014An efficient alternative to SPIDER3\u2010single for sequence\u2010based prediction of protein secondary structures","display_name":"ProteinUnet\u2014An efficient alternative to SPIDER3\u2010single for sequence\u2010based prediction of protein secondary structures","publication_year":2020,"publication_date":"2020-10-15","ids":{"openalex":"https://openalex.org/W3093108887","doi":"https://doi.org/10.1002/jcc.26432","mag":"3093108887","pmid":"https://pubmed.ncbi.nlm.nih.gov/33058261","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7756333"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1002/jcc.26432","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.26432","source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.26432","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069610379","display_name":"Krzysztof Kotowski","orcid":"https://orcid.org/0000-0003-2596-6517"},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Krzysztof Kotowski","raw_affiliation_string":"Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland","raw_affiliation_strings":["Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070421166","display_name":"Tomasz Smolarczyk","orcid":null},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Tomasz Smolarczyk","raw_affiliation_string":"Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland","raw_affiliation_strings":["Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061129851","display_name":"Irena Roterman-Konieczna","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Irena Roterman-Konieczna","raw_affiliation_string":"Department of Bioinformatics and Telemedicine Jagiellonian University Medical College Krak\u00f3w Poland","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine Jagiellonian University Medical College Krak\u00f3w Poland"]},{"author_position":"last","author":{"id":"https://openalex.org/A5045740283","display_name":"Katarzyna St\u0105por","orcid":"https://orcid.org/0000-0003-3003-6592"},"institutions":[{"id":"https://openalex.org/I119004910","display_name":"Silesian University of Technology","ror":"https://ror.org/02dyjk442","country_code":"PL","type":"education","lineage":["https://openalex.org/I119004910"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Katarzyna Stapor","raw_affiliation_string":"Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland","raw_affiliation_strings":["Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland"]}],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045740283"],"corresponding_institution_ids":["https://openalex.org/I119004910"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840,"provenance":"doaj"},"apc_paid":{"value":4840,"currency":"USD","value_usd":4840,"provenance":"doaj"},"has_fulltext":false,"cited_by_count":18,"cited_by_percentile_year":{"min":93,"max":94},"biblio":{"volume":"42","issue":"1","first_page":"50","last_page":"59"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure Prediction and Analysis","score":0.9997,"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 Prediction and Analysis","score":0.9997,"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":"Prediction of Protein Subcellular Localization","score":0.9994,"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":"Ribosome Structure and Translation Mechanisms","score":0.9977,"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":[{"keyword":"proteinunet\u2014an","score":0.4281}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7523354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.639516},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6345734},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.58349335},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.50095654},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.495515},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47509253},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.4731078},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4680616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3441754},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33342987},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17964154},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10134214},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1002/jcc.26432","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.26432","source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/264487","pdf_url":"https://ruj.uj.edu.pl/xmlui/bitstream/handle/item/264487/roterman-konieczna_et-al_proteinunet-an_efficient_alternative_to_spider3-single_2021.pdf?sequence=1&isAllowed=y","source":{"id":"https://openalex.org/S4306400316","display_name":"Homo Politicus (Academy of Humanities and Economics in Lodz)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756333","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,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":["National Institutes of Health"],"type":"repository"},"license":null,"version":"publishedVersion","is_accepted":true,"is_published":true}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1002/jcc.26432","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.26432","source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[],"referenced_works_count":33,"referenced_works":["https://openalex.org/W109897823","https://openalex.org/W1901129140","https://openalex.org/W1963741981","https://openalex.org/W1999724806","https://openalex.org/W2008708467","https://openalex.org/W2041369927","https://openalex.org/W2045777307","https://openalex.org/W2051210555","https://openalex.org/W2051872583","https://openalex.org/W2061663059","https://openalex.org/W2064675550","https://openalex.org/W2100908214","https://openalex.org/W2114850508","https://openalex.org/W2130479394","https://openalex.org/W2140992384","https://openalex.org/W2143197682","https://openalex.org/W2143210482","https://openalex.org/W2153153865","https://openalex.org/W2158714788","https://openalex.org/W2574496196","https://openalex.org/W2607268717","https://openalex.org/W2739202500","https://openalex.org/W2898320067","https://openalex.org/W2915893085","https://openalex.org/W2963174729","https://openalex.org/W2965837840","https://openalex.org/W2968700072","https://openalex.org/W2970658101","https://openalex.org/W2980272550","https://openalex.org/W2980699342","https://openalex.org/W2986661129","https://openalex.org/W2991257700","https://openalex.org/W3023726311"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2052835778","https://openalex.org/W2049003611","https://openalex.org/W2127804977","https://openalex.org/W2108418243","https://openalex.org/W164103134","https://openalex.org/W2787352659","https://openalex.org/W1970611213","https://openalex.org/W4206560911","https://openalex.org/W4372260270"],"ngrams_url":"https://api.openalex.org/works/W3093108887/ngrams","abstract_inverted_index":{"Abstract":[0],"Predicting":[1],"protein":[2],"function":[3],"and":[4,38,91,95,110,126],"structure":[5],"from":[6,23],"sequence":[7,25,42],"remains":[8],"an":[9,59,144],"unsolved":[10],"problem":[11],"in":[12],"bioinformatics.":[13],"The":[14],"best":[15],"performing":[16],"methods":[17,80],"rely":[18],"heavily":[19],"on":[20,71],"evolutionary":[21],"information":[22],"multiple":[24],"alignments,":[26],"which":[27],"means":[28],"their":[29],"accuracy":[30,149],"deteriorates":[31],"for":[32,84,123,150],"sequences":[33,125],"with":[34,128],"a":[35,50,129],"few":[36],"homologs,":[37],"given":[39],"the":[40,136],"increasing":[41,148],"database":[43],"sizes":[44],"requires":[45],"long":[46,72],"computation":[47],"times.":[48],"Here,":[49],"single\u2010sequence\u2010based":[51],"prediction":[52,85],"method":[53,137],"is":[54,65,141],"presented,":[55],"called":[56],"ProteinUnet,":[57],"leveraging":[58],"U\u2010Net":[60],"convolutional":[61],"network":[62],"architecture.":[63,78],"It":[64],"compared":[66],"to":[67,120],"SPIDER3\u2010Single":[68],"model,":[69],"based":[70],"short\u2010term":[73],"memory\u2010bidirectional":[74],"recurrent":[75],"neural":[76],"networks":[77],"Both":[79],"achieve":[81],"similar":[82],"results":[83],"of":[86,132,138,147],"secondary":[87,152],"structures":[88],"(both":[89],"three\u2010":[90],"eight\u2010state),":[92],"half\u2010sphere":[93],"exposure,":[94],"contact":[96],"number,":[97],"but":[98],"ProteinUnet":[99,118],"has":[100],"two":[101],"times":[102,106,115],"fewer":[103],"parameters,":[104],"17":[105],"shorter":[107],"inference":[108],"time,":[109],"can":[111],"be":[112,121],"trained":[113],"11":[114],"faster.":[116],"Moreover,":[117],"tends":[119],"better":[122],"short":[124],"residues":[127],"low":[130],"number":[131],"local":[133],"contacts.":[134],"Additionally,":[135],"loss":[139],"weighting":[140],"presented":[142],"as":[143],"effective":[145],"way":[146],"rare":[151],"structures.":[153]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W3093108887","counts_by_year":[{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":3}],"updated_date":"2024-03-21T10:16:39.433147","created_date":"2020-10-22"}