Docking of 8400 peptides into an experimental structure of bacterial peptide transporter DtpB

Di- and tripeptides composed of proteinogenic amino acids were docked into an experimental structure of DtpB using Rosetta FlexPepDock protocol. Additional experimental structures of DtpB were used to train a classifier to select top docking poses. Average Rosetta energy terms for top 10 hits were then combined with experimental affinity measurements to train a binary classifier that predicts binders to DtpB.

This upload includes input and output data as well as code to run and analyse the full pipeline. Some intermediate results are available upon request.

For more details, please see:
Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition

https://dx.doi.org/10.1016/j.celrep.2023.112831