Welcome to the Poké user guide

This guide documents Poké 0.1.1.

Poké scouter is a blazing fast pocket scouter based on CHARMM forcefield. It uses an energy-based approach to identify the low-energy regions of the protein and it is able to compute a set of descriptors for each pocket useful to characterize it. The descriptors are used then by a neural network model to assign a druggability score to the pocket.

Designed to be used on long molecular dynamics trajectories, but it can be used also on single frames.

Get Started

If you are new to Poké, start here:

• Getting Started to install the package and run it on a structure or a trajectory

• Tutorials for a worked example on a cryptic pocket of TEM-1 β-lactamase

How to cite

If you use Poké in your research, please cite:

Colasurdo, E., Boldrini, A., Terruzzi, L., Langini, C., Risueño Fernández, C., Varricchio, C., Primavera, E., Cassese, E., Patsilinakos, A. & Spagnolli, G. Poké: Fast and Reliable Neural-Network-Based Identification of Protein Ligandable Sites. ACS Omega (2026). https://doi.org/10.1021/acsomega.6c04816

Code and data

• Source code on GitHub: https://github.com/SibyllaBiotech/poke

• Source code archived on Zenodo: https://doi.org/10.5281/zenodo.19634786

• Datasets used in the paper, on Zenodo: https://doi.org/10.5281/zenodo.19635030

Licence

Poké is free software released under the MIT licence. The text and figures of this guide are released under the CC BY 4.0 licence.