MAGPIE: Mapping Areas of Genetic Parsimony In Epitopes

MAGPIE is a tool for analyzing thousands of protein-ligand interactions at once. It generates an interactive 3D visualization from a set of protein complex structures that share a target ligand, as well as sequence logo-style frequency graphs. These graphs show all the amino acids from the set of protein binders that interact with user-selected target ligand positions. MAGPIE is compatible with both small molecule and protein ligands.

Contents:

I. Introduction

• What is this MAGPIE?

II. Inputs

• Required inputs

III. Using MAGPIE via GoogleColab

• Using MAGPIE with GoogleColab

IV. Installing and Using MAGPIE via Local-Version

• Using MAGPIE with Local-Version

V. Using the MAGPIE GUI

• Using the MAGPIE GUI

VI. Preparing your own dataset for use in MAGPIE

• Preparing your own dataset for use in MAGPIE

VII. Description of Helper scripts

• Helper Scripts