{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T17:11:44Z","timestamp":1773162704164,"version":"3.50.1"},"reference-count":115,"publisher":"World Scientific Pub Co Pte Ltd","issue":"01","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2011,2]]},"abstract":"<jats:p>Proteases have central roles in \"life and death\" processes due to their important ability to catalytically hydrolyze protein substrates, usually altering the function and\/or activity of the target in the process. Knowledge of the substrate specificity of a protease should, in theory, dramatically improve the ability to predict target protein substrates. However, experimental identification and characterization of protease substrates is often difficult and time-consuming. Thus solving the \"substrate identification\" problem is fundamental to both understanding protease biology and the development of therapeutics that target specific protease-regulated pathways. In this context, bioinformatic prediction of protease substrates may provide useful and experimentally testable information about novel potential cleavage sites in candidate substrates. In this article, we provide an overview of recent advances in developing bioinformatic approaches for predicting protease substrate cleavage sites and identifying novel putative substrates. We discuss the advantages and drawbacks of the current methods and detail how more accurate models can be built by deriving multiple sequence and structural features of substrates. We also provide some suggestions about how future studies might further improve the accuracy of protease substrate specificity prediction.<\/jats:p>","DOI":"10.1142\/s0219720011005288","type":"journal-article","created":{"date-parts":[[2010,11,3]],"date-time":"2010-11-03T08:33:53Z","timestamp":1288773233000},"page":"149-178","source":"Crossref","is-referenced-by-count":35,"title":["BIOINFORMATIC APPROACHES FOR PREDICTING SUBSTRATES OF PROTEASES"],"prefix":"10.1142","volume":"09","author":[{"given":"JIANGNING","family":"SONG","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia"},{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan"},{"name":"Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China"}]},{"given":"HAO","family":"TAN","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia"}]},{"given":"SARAH E.","family":"BOYD","sequence":"additional","affiliation":[{"name":"AgriBio, La Trobe University, Victoria 3086, Australia"}]},{"given":"HONGBIN","family":"SHEN","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200240, China"}]},{"given":"KHALID","family":"MAHMOOD","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia"},{"name":"ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Victoria 3800, Australia"}]},{"given":"GEOFFREY I.","family":"WEBB","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology, Monash University, Victoria 3800, Australia"}]},{"given":"TATSUYA","family":"AKUTSU","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan"}]},{"given":"JAMES C.","family":"WHISSTOCK","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia"},{"name":"ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Victoria 3800, Australia"}]},{"given":"ROBERT N.","family":"PIKE","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm954"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1038\/nrd2092"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1038\/nrc2228"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn570"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1038\/nrm858"},{"key":"rf6","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1515\/BC.2009.065","volume":"390","author":"Ng N. 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