SIP: Self-Inhibitory Peptides

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4 SIP: Self-inhibitory peptide design
SIP’s inputs are the protein fasta sequence and the PDB file.
We have the sequences and the PDB files for all proteins that have been successfully aligned with active peptides. We design self-inhibitory peptides targeting these proteins using SIP. The process consists in four steps that will be briefly described here: The first step is the secondary structure prediction followed by the second step, which is the disorder prediction. These first two steps are based on the protein sequence only. The third step is the selection of segments of 20 amino acid long, with low disorder and helical secondary structure, within the protein. And finally, the fourth step is the calculation of the the energy score based of the structural information from the PDB file.
A good candidate self-inhibitory peptide must have a stable secondary structure.
To be realistically considered as good candidate self-inhibitory peptides, they should be as stable as possible. That’s why SIP selects segments of the target protein that are 20 amino-acid long with helical secondary structure and low disorder probability.
A good candidate self-inhibitory peptide must have a strong interaction energy with the protein target.
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It is the most important criteria to determine if the segment is a good potential self-inhibitory peptide or not. The lower the energy score, the stronger the interaction is likely to be between the self-inhibitory peptide and the protein target. To discriminate a good self-inhibitory peptide from a weak one, we set a threshold value of -40 for the energy score. Segments with an energy score below this threshold are considered as good candidate self-inhibitory
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