Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.08.01.551496v1?rss=1
Authors: GUYON, F., Moroy, G.
Abstract:
Motivation: Peptides are molecules involved in many essential biological activities by interacting with proteins in the body. They can also be used as therapeutic molecules, particularly to disrupt protein-protein interactions involved in disease. However, it is difficult to identify potential therapeutic peptides if the structure of the protein-protein complex to be inhibited has not been solved. Results: The PepIT program was developed to propose peptides that can interact with a given protein. PepIT is based on a non-sequential alignment algorithm to identify peptide binding sites that share geometrical and physicochemical properties with a surface region of the target protein. PepIT compares the entire surface of the target protein with the peptide binding sites of the Propedia dataset, which contains more than 19,000 high-resolution protein-peptide structures. Once a peptide binding site similar to a portion of the protein surface is found, the peptide bound to the binding site is repositioned on the corresponding portion of the protein surface. Availability and implementation: The PepIT source code is freely available at https://github.com/DSIMB/pepit
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