{"id":"https://openalex.org/W2890951984","doi":"https://doi.org/10.1093/bib/bby077","title":"Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods","display_name":"Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods","publication_year":2018,"publication_date":"2018-08-03","ids":{"openalex":"https://openalex.org/W2890951984","doi":"https://doi.org/10.1093/bib/bby077","mag":"2890951984","pmid":"https://pubmed.ncbi.nlm.nih.gov/30184176"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby077","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby077","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/20.500.11850/391771","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063409460","display_name":"Fuyi Li","orcid":"https://orcid.org/0000-0001-5216-3213"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Fuyi Li","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100385375","display_name":"Yanan Wang","orcid":"https://orcid.org/0000-0002-3820-8443"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Yanan Wang","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100369818","display_name":"Chen Li","orcid":"https://orcid.org/0000-0002-1847-754X"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","CH"],"is_corresponding":false,"raw_author_name":"Chen Li","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","Department of Biology, Institute of Molecular Systems Biology,ETH Z\u00fcrich, Z\u00fcrich 8093, Switzerland"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology,ETH Z\u00fcrich, Z\u00fcrich 8093, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042243195","display_name":"Tatiana T. Marquez\u2010Lago","orcid":"https://orcid.org/0000-0003-3279-5592"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tatiana T Marquez-Lago","raw_affiliation_strings":["Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042438246","display_name":"Andr\u00e9 Leier","orcid":"https://orcid.org/0000-0002-2647-2693"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Leier","raw_affiliation_strings":["Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051168121","display_name":"Neil D. Rawlings","orcid":"https://orcid.org/0000-0001-5557-7665"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Neil D Rawlings","raw_affiliation_strings":["EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081525024","display_name":"Gholamreza Haffari","orcid":"https://orcid.org/0000-0001-7326-8380"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Gholamreza Haffari","raw_affiliation_strings":["Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059942694","display_name":"Jerico Revote","orcid":"https://orcid.org/0000-0002-0381-3600"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jerico Revote","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113500576","display_name":"Kuo\u2010Chen Chou","orcid":null},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]},{"id":"https://openalex.org/I4210098239","display_name":"The Gordon Life Science Institute","ror":"https://ror.org/0135ffj82","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098239"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Kuo-Chen Chou","raw_affiliation_strings":["Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China","Gordon Life Science Institute, Boston, MA 02478, USA"],"affiliations":[{"raw_affiliation_string":"Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China","institution_ids":["https://openalex.org/I150229711"]},{"raw_affiliation_string":"Gordon Life Science Institute, Boston, MA 02478, USA","institution_ids":["https://openalex.org/I4210098239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087347737","display_name":"Anthony W. Purcell","orcid":"https://orcid.org/0000-0003-0532-8331"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Anthony W Purcell","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030866932","display_name":"Robert N. Pike","orcid":"https://orcid.org/0000-0002-2083-0269"},"institutions":[{"id":"https://openalex.org/I196829312","display_name":"La Trobe University","ror":"https://ror.org/01rxfrp27","country_code":"AU","type":"education","lineage":["https://openalex.org/I196829312"]},{"id":"https://openalex.org/I4210146297","display_name":"ARC Centre of Excellence in Advanced Molecular Imaging","ror":"https://ror.org/051e7s436","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Robert N Pike","raw_affiliation_strings":["ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"raw_affiliation_string":"La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia","institution_ids":["https://openalex.org/I196829312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058054791","display_name":"Geoffrey I. Webb","orcid":"https://orcid.org/0000-0001-9963-5169"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Geoffrey I Webb","raw_affiliation_strings":["Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048164886","display_name":"A. Ian Smith","orcid":"https://orcid.org/0000-0002-4143-2892"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I4210146297","display_name":"ARC Centre of Excellence in Advanced Molecular Imaging","ror":"https://ror.org/051e7s436","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"A Ian Smith","raw_affiliation_strings":["ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004968684","display_name":"Trevor Lithgow","orcid":"https://orcid.org/0000-0002-0102-7884"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Trevor Lithgow","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060521527","display_name":"Roger J. Daly","orcid":"https://orcid.org/0000-0002-5739-8027"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Roger J Daly","raw_affiliation_strings":["Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050620343","display_name":"James C. Whisstock","orcid":"https://orcid.org/0000-0003-4200-5611"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I4210146297","display_name":"ARC Centre of Excellence in Advanced Molecular Imaging","ror":"https://ror.org/051e7s436","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"James C Whisstock","raw_affiliation_strings":["ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012709797","display_name":"Jiangning Song","orcid":"https://orcid.org/0000-0001-8031-9086"},"institutions":[{"id":"https://openalex.org/I2801239119","display_name":"Australian Regenerative Medicine Institute","ror":"https://ror.org/02qa5kg76","country_code":"AU","type":"facility","lineage":["https://openalex.org/I2801037857","https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I4210146297","display_name":"ARC Centre of Excellence in Advanced Molecular Imaging","ror":"https://ror.org/051e7s436","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Jiangning Song","raw_affiliation_strings":["ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I4210146297","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":18,"corresponding_author_ids":["https://openalex.org/A5012709797","https://openalex.org/A5050620343"],"corresponding_institution_ids":["https://openalex.org/I2801239119","https://openalex.org/I4210146297","https://openalex.org/I56590836"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.1438,"has_fulltext":false,"cited_by_count":102,"citation_normalized_percentile":{"value":0.97381391,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"20","issue":"6","first_page":"2150","last_page":"2166"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T13637","display_name":"Calpain Protease Function and Regulation","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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":0.9896000027656555,"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/cleavage","display_name":"Cleavage (geology)","score":0.5924733877182007},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5885598659515381},{"id":"https://openalex.org/keywords/proteases","display_name":"Proteases","score":0.5776907801628113},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5642516016960144},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.5466216206550598},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.49878621101379395},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48817259073257446},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.47054463624954224},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.4503157138824463},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43176060914993286},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3811977505683899},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34111249446868896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2154698371887207},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15192699432373047},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12794229388237},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.11101236939430237}],"concepts":[{"id":"https://openalex.org/C175156509","wikidata":"https://www.wikidata.org/wiki/Q1990218","display_name":"Cleavage (geology)","level":3,"score":0.5924733877182007},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5885598659515381},{"id":"https://openalex.org/C182220744","wikidata":"https://www.wikidata.org/wiki/Q7251226","display_name":"Proteases","level":3,"score":0.5776907801628113},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5642516016960144},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.5466216206550598},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.49878621101379395},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48817259073257446},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.47054463624954224},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.4503157138824463},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43176060914993286},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3811977505683899},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34111249446868896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2154698371887207},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15192699432373047},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12794229388237},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.11101236939430237},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C43369102","wikidata":"https://www.wikidata.org/wiki/Q2307625","display_name":"Fracture (geology)","level":2,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bby077","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby077","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30184176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30184176","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:digital.library.adelaide.edu.au:2440/139588","is_oa":false,"landing_page_url":"https://hdl.handle.net/2440/139588","pdf_url":null,"source":{"id":"https://openalex.org/S4306401835","display_name":"Adelaide Research & Scholarship (AR&S) (University of Adelaide)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5681781","host_organization_name":"The University of Adelaide","host_organization_lineage":["https://openalex.org/I5681781"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dx.doi.org/10.1093/bib/bby077","raw_type":"Journal article"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:86d47b5","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5915380","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6954447","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/391771","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/391771","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 20 (6)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000391771","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000391771","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/391771","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/391771","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 20 (6)","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1127919792","display_name":null,"funder_award_id":"DP120104460","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G241248248","display_name":null,"funder_award_id":"LP110200333","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G2482007926","display_name":null,"funder_award_id":"AI111965","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4162901504","display_name":null,"funder_award_id":"2018-28","funder_id":"https://openalex.org/F4320320971","funder_display_name":"Monash University"},{"id":"https://openalex.org/G8874312312","display_name":null,"funder_award_id":"1092262","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320310431","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205"},{"id":"https://openalex.org/F4320320971","display_name":"Monash University","ror":"https://ror.org/02bfwt286"},{"id":"https://openalex.org/F4320323365","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":135,"referenced_works":["https://openalex.org/W605727707","https://openalex.org/W1536886974","https://openalex.org/W1594031697","https://openalex.org/W1965179332","https://openalex.org/W1966581230","https://openalex.org/W1968178167","https://openalex.org/W1968959655","https://openalex.org/W1972245778","https://openalex.org/W1973445088","https://openalex.org/W1977046764","https://openalex.org/W1985469117","https://openalex.org/W1990306877","https://openalex.org/W1990695683","https://openalex.org/W1991263759","https://openalex.org/W1993548347","https://openalex.org/W1994830145","https://openalex.org/W1997104566","https://openalex.org/W2001349696","https://openalex.org/W2002798380","https://openalex.org/W2002960388","https://openalex.org/W2010601153","https://openalex.org/W2011339859","https://openalex.org/W2015981827","https://openalex.org/W2024069545","https://openalex.org/W2030060549","https://openalex.org/W2033427731","https://openalex.org/W2038916773","https://openalex.org/W2042409347","https://openalex.org/W2044765456","https://openalex.org/W2049387903","https://openalex.org/W2053632669","https://openalex.org/W2060470491","https://openalex.org/W2060629279","https://openalex.org/W2064675550","https://openalex.org/W2071095496","https://openalex.org/W2071874518","https://openalex.org/W2076015897","https://openalex.org/W2076063813","https://openalex.org/W2082702196","https://openalex.org/W2088569816","https://openalex.org/W2091194259","https://openalex.org/W2092743216","https://openalex.org/W2100638553","https://openalex.org/W2100805904","https://openalex.org/W2103525038","https://openalex.org/W2103700658","https://openalex.org/W2107641306","https://openalex.org/W2114543843","https://openalex.org/W2116876798","https://openalex.org/W2117299753","https://openalex.org/W2118185751","https://openalex.org/W2119531440","https://openalex.org/W2122460814","https://openalex.org/W2123903570","https://openalex.org/W2123958887","https://openalex.org/W2125055259","https://openalex.org/W2135293965","https://openalex.org/W2136575978","https://openalex.org/W2139492479","https://openalex.org/W2147880316","https://openalex.org/W2148528976","https://openalex.org/W2149414426","https://openalex.org/W2150245222","https://openalex.org/W2152365098","https://openalex.org/W2154053567","https://openalex.org/W2157062944","https://openalex.org/W2159972803","https://openalex.org/W2160965492","https://openalex.org/W2166512255","https://openalex.org/W2168012258","https://openalex.org/W2170283814","https://openalex.org/W2171071516","https://openalex.org/W2248525918","https://openalex.org/W2268048347","https://openalex.org/W2310259903","https://openalex.org/W2311607323","https://openalex.org/W2316370427","https://openalex.org/W2325374849","https://openalex.org/W2471196942","https://openalex.org/W2508883697","https://openalex.org/W2514430732","https://openalex.org/W2528774686","https://openalex.org/W2559947248","https://openalex.org/W2573949625","https://openalex.org/W2576005654","https://openalex.org/W2577194649","https://openalex.org/W2583310064","https://openalex.org/W2587688848","https://openalex.org/W2592839484","https://openalex.org/W2593430295","https://openalex.org/W2595697910","https://openalex.org/W2605763657","https://openalex.org/W2608270353","https://openalex.org/W2735302890","https://openalex.org/W2737592062","https://openalex.org/W2742750032","https://openalex.org/W2742760452","https://openalex.org/W2743021819","https://openalex.org/W2747811776","https://openalex.org/W2765207150","https://openalex.org/W2766389776","https://openalex.org/W2768022300","https://openalex.org/W2769449671","https://openalex.org/W2791600746","https://openalex.org/W2792363117","https://openalex.org/W2793168264","https://openalex.org/W2794004073","https://openalex.org/W2794273483","https://openalex.org/W2794797435","https://openalex.org/W2800333284","https://openalex.org/W2805791355","https://openalex.org/W2806931818","https://openalex.org/W2808950870","https://openalex.org/W2810225085","https://openalex.org/W2886761756","https://openalex.org/W2911964244","https://openalex.org/W4206192903","https://openalex.org/W4232478844","https://openalex.org/W4297957988","https://openalex.org/W6632243507","https://openalex.org/W6668318749","https://openalex.org/W6669214369","https://openalex.org/W6678254130","https://openalex.org/W6683226453","https://openalex.org/W6697974936","https://openalex.org/W6698064614","https://openalex.org/W6732096850","https://openalex.org/W6732543502","https://openalex.org/W6733365994","https://openalex.org/W6742377446","https://openalex.org/W6745226055","https://openalex.org/W6751150484","https://openalex.org/W6752385622","https://openalex.org/W6754209133","https://openalex.org/W6928872010"],"related_works":["https://openalex.org/W2182122486","https://openalex.org/W2109018839","https://openalex.org/W1596676072","https://openalex.org/W2068975409","https://openalex.org/W3207552102","https://openalex.org/W124183450","https://openalex.org/W2153970031","https://openalex.org/W2159000061","https://openalex.org/W232194933","https://openalex.org/W2071182206"],"abstract_inverted_index":{"The":[0,190],"roles":[1],"of":[2,28,43,54,64,81,131,147,170],"proteolytic":[3,55],"cleavage":[4,86,103,184,207,218,279],"have":[5,46,75],"been":[6,21,47,76],"intensively":[7],"investigated":[8],"and":[9,39,60,84,112,140,155,168,211,235,249,251,265],"discussed":[10],"during":[11],"the":[12,52,61,97,109,115,166,171,198,232,237],"past":[13],"two":[14],"decades.":[15],"This":[16],"irreversible":[17],"chemical":[18],"process":[19],"has":[20],"frequently":[22],"reported":[23],"to":[24,94,106,113,164,187,230,271],"influence":[25],"a":[26,129,263],"number":[27,42,63],"crucial":[29],"biological":[30],"processes":[31],"(BPs),":[32],"such":[33],"as":[34,262],"cell":[35],"cycle,":[36],"protein":[37],"regulation":[38],"inflammation.":[40],"A":[41],"advanced":[44],"studies":[45],"published":[48],"aiming":[49],"at":[50],"deciphering":[51],"mechanisms":[53],"cleavage.":[56],"Given":[57],"its":[58],"significance":[59],"large":[62],"functionally":[65],"enriched":[66],"substrates":[67,83],"targeted":[68],"by":[69,240],"specific":[70],"proteases,":[71],"many":[72],"computational":[73,99,133,238],"approaches":[74,100],"established":[77],"for":[78,101,203,216,268,277],"accurate":[79,200],"prediction":[80,105,116,233],"protease-specific":[82,102,206,278],"their":[85,148],"sites.":[87,219],"Consequently,":[88],"there":[89],"is":[90,197],"an":[91],"urgent":[92],"need":[93],"systematically":[95],"assess":[96,165],"state-of-the-art":[98],"site":[104,280],"further":[107,272],"advance":[108,273],"existing":[110],"methodologies":[111],"improve":[114,231],"performance.":[117],"With":[118],"this":[119,124],"goal":[120],"in":[121,123,145],"mind,":[122],"article,":[125],"we":[126,224],"carefully":[127,176],"evaluated":[128],"total":[130],"19":[132],"methods":[134,139,173],"(including":[135],"8":[136],"scoring":[137],"function-based":[138],"11":[141],"machine":[142],"learning-based":[143],"methods)":[144],"terms":[146],"underlying":[149],"algorithm,":[150],"calculated":[151],"features,":[152],"performance":[153,234],"evaluation":[154],"software":[156],"usability.":[157],"Then,":[158],"extensive":[159],"independent":[160,178],"tests":[161],"were":[162],"performed":[163],"robustness":[167],"scalability":[169],"reviewed":[172],"using":[174],"our":[175,222,258],"prepared":[177],"test":[179],"data":[180],"sets":[181],"with":[182],"3641":[183],"sites":[185],"(specific":[186],"10":[188],"proteases).":[189],"comparative":[191],"experimental":[192],"results":[193],"demonstrate":[194],"that":[195,257],"PROSPERous":[196],"most":[199],"generic":[201],"method":[202],"predicting":[204],"eight":[205],"sites,":[208],"while":[209],"GPS-CCD":[210],"LabCaS":[212],"outperformed":[213],"other":[214],"predictors":[215],"calpain-specific":[217],"Based":[220],"on":[221],"review,":[223],"then":[225],"outlined":[226],"some":[227],"potential":[228],"ways":[229],"ease":[236],"burden":[239],"applying":[241],"ensemble":[242],"learning,":[243,245],"deep":[244],"positive":[246],"unlabeled":[247],"learning":[248],"parallel":[250],"distributed":[252],"computing":[253],"techniques.":[254],"We":[255],"anticipate":[256],"study":[259],"will":[260],"serve":[261],"practical":[264],"useful":[266],"guide":[267],"interested":[269],"readers":[270],"next-generation":[274],"bioinformatics":[275],"tools":[276],"prediction.":[281]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":23},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
