Introduction

For some target proteins, available static structures may lack obvious small molecule binding sites, or visible pockets may have properties (e.g., high intrafamily similarity) that make them challenging for drug development. The OpenEye Cryptic Pocket Detection Floes aim to uncover hidden binding sites and help assess the druggability of such difficult targets. They do this by sampling protein dynamics using weighted ensemble molecular dynamics (MD) simulations [Zuckerman-2017], then analyzing the resulting trajectory data to identify potential cryptic pockets. When successful, these floes enable the use of other OpenEye discovery tools.

For details on the methods used in this package, please refer to the accompanying webinar: “Efficient protein conformational sampling and the automated identification of cryptic pockets.”