Protein recognition of particular molecules is a key biological function that is important for a variety of applications. A major goal is the ability to alter binding, which can be accomplished by reusing recognised interaction motifs.A method for creating peptide binding modules was of particular interest to us.
The authors intend to speed up the design of new protein or peptide binders by utilising interaction data from recognised protein structures.To help the investigation and design of a protein’s interaction with a single side chain, Kynast J.P. et. al. (2022) created the computer approach ATLIGATOR. Based on structures from the PDB, their tool enables the construction of interaction atlases.Pocket definitions that can be searched for common interactions are taken from these atlases.
The source code can be obtained from the following website https://www.github.com/Hoecker-Lab/atligator
Reference:
Kynast J.P. et. al. (2022) ATLIGATOR: editing protein interactions with an atlas-based approach. Bioinformatics 38(23): 5199-5205.