![]() The malfunction or deregulation of proteases results in many pathological conditions. Pepsin, trypsin and chymotrypsin also come into this category, even though they have a defined specificity because they degrade so many substrates, most of which are foreign to the body. In addition, these are also many other proteases involved in protein degradation rather than processing, for example cathepsin D and cathepsin B. Through the highly selective proteolytic processing, proteases can precisely regulate a myriad of biological processes across all living organisms. Proteases have central roles in ‘life or death’ processes. This process is controlled by proteases (also known as peptidases or proteinases) that selectively cleave the peptide bonds between amino acids in specific protein or peptide substrates. It plays a key role in numerous developmental and physiological processes, including digestion, protein degradation, endocrine signaling and cell division. protease, substrate, cleavage site, sequence analysis, machine learning, five-step rule Introduction Proteolytic cleavage is one of the few irreversible posttranslational modifications. We anticipate that iProt-Sub will be a powerful tool for proteome-wide prediction of protease-specific substrates and their cleavage sites, and will facilitate hypothesis-driven functional interrogation of protease-specific substrate cleavage and proteolytic events. Benchmarking experiments using cross-validation and independent tests showed that iProt-Sub is able to achieve a better performance than several existing generic tools. Features used by iProt-Sub are encoded by 11 different sequence encoding schemes, including local amino acid sequence profile, secondary structure, solvent accessibility and native disorder, which will allow a more accurate representation of the protease specificity of approximately 38 proteases and training of the prediction models. ![]() iProt-Sub integrates heterogeneous sequence and structural features and uses a two-step feature selection procedure to further remove redundant and irrelevant features in an effort to improve the cleavage site prediction accuracy. ![]() It provides optimized cleavage site prediction models with better prediction performance and coverage for more species-specific proteases (4 major protease families and 38 different proteases). Importantly, iProt-Sub represents a significantly advanced version of its successful predecessor, PROSPER. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the accurate prediction of protease-specific substrates and their cleavage sites. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. Song, Jiangning Wang, Yanan Li, Fuyi Akutsu, Tatsuya Rawlings, Neil D Webb, Geoffrey I Chou, Kuo-ChenĪbstract Regulation of proteolysis plays a critical role in a myriad of important cellular processes. IProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific.
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