{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T02:00:30Z","timestamp":1776132030348,"version":"3.50.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:\u2003Caspases and granzyme B (GrB) are important proteases involved in fundamental cellular processes and play essential roles in programmed cell death, necrosis and inflammation. Although a number of substrates for both types have been experimentally identified, the complete repertoire of caspases and granzyme B substrates remained to be fully characterized. Accordingly, systematic bioinformatics studies of known cleavage sites may provide important insights into their substrate specificity and facilitate the discovery of novel substrates.<\/jats:p>\n               <jats:p>Results:\u2003We develop a new bioinformatics tool, termed Cascleave 2.0, which builds on previous success of the Cascleave tool for predicting generic caspase cleavage sites. It can be efficiently used to predict potential caspase-specific cleavage sites for the human caspase-1, 3, 6, 7, 8 and GrB. In particular, we integrate heterogeneous sequence and protein functional information from various sources to improve the prediction accuracy of Cascleave 2.0. During classification, we use both maximum relevance minimum redundancy and forward feature selection techniques to quantify the relative contribution of each feature to prediction and thus remove redundant as well as irrelevant features. A systematic evaluation of Cascleave 2.0 using the benchmark data and comparison with other state-of-the-art tools using independent test data indicate that Cascleave 2.0 outperforms other tools on protease-specific cleavage site prediction of caspase-1, 3, 6, 7 and GrB. Cascleave 2.0 is anticipated to be used as a powerful tool for identifying novel substrates and cleavage sites of caspases and GrB and help understand the functional roles of these important proteases in human proteolytic cascades.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003http:\/\/www.structbioinfor.org\/cascleave2\/.<\/jats:p>\n               <jats:p>Contact:\u2003Jiangning.Song@monash.edu or James.Whisstock@monash.edu<\/jats:p>\n               <jats:p>Supplementary information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt603","type":"journal-article","created":{"date-parts":[[2013,10,23]],"date-time":"2013-10-23T01:14:23Z","timestamp":1382490863000},"page":"71-80","source":"Crossref","is-referenced-by-count":69,"title":["Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets"],"prefix":"10.1093","volume":"30","author":[{"given":"Mingjun","family":"Wang","sequence":"first","affiliation":[{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"},{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xing-Ming","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Tan","sequence":"additional","affiliation":[{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James C.","family":"Whisstock","sequence":"additional","affiliation":[{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"},{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"},{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"},{"name":"1 National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, 2Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, 3Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, 4Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan and 5ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,10,21]]},"reference":[{"key":"2023012710381029300_btt603-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and 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