As part of a recently published statistical analysis of approximately 30,000 substrates of cathepsins K, V, B, L, S and F, we have developed the SAPS-ESI (“Statistical Approach to Specific Peptide Substrate-Enzyme Interaction”) software platform, which contains new approaches and algorithms for determining the specificity of positions near the cleavage sites, classifying substrates into groups, determining the connection of amino acids at different positions (cooperativity) and predicting cleavage sites (Tušar et al, 2023). We plan to upgrade the software platform with new methods and algorithms.
The goals of this work will be:
- upgrade of the SAPS – ESI software platform for the study of peptide substrate – enzyme interactions (in the Python 3.x programming language),
- analyze data from additional databases,
- development of new statistical and bioinformatic approaches for the study of the mentioned interactions,
- establish involvement of cysteine cathepsins and other enzymes in yet unexplored physiological pathways.
References
- Turk et al., Cysteine cathepsins: from structure, function and regulation to new frontiers. Biochimica et biophysica acta 1824, 68-88 (2012).
- Tušar L. et al., Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Communications biology 6, 450 (2023).