appraise 1.2

Scripts and functions needed for for APPARISE.

APPRAISE

Automated Pair-wise Peptide-Receptor binding model AnalysIs for Screening Engineered proteins (APPRAISE) is a method that predicts the receptor binding propensity of engineered proteins based on high-precision protein structure prediction tools, such as AlphaFold2-multimer. This Python package includes tools for preparing input files and analyzing the modeled structures.

Author: Xiaozhe Ding (Email: [e-mail], [e-mail]; Twitter: @DingXiaozhe)

Environment

APPRAISE 1.2 was tested with the following environment:

• MacOS 10.14.6

• Python 3.6.10

• Alphafold-colabfold 2.1.14 (Available here)

• PyMOL 2.3.3 (Schrodinger LLC.)

• Python packages:

  • scipy 1.4.1

  • numpy 1.18.2

  • pandas 1.1.5

  • matplotlib 3.2.1

  • seaborn 0.11.2

Installation

Option 1 (recommended)

Install the distribution from PyPI. In the terminal, run:

pip install appraise

Option 2 (back-up)

Download the repository to your local computer and unzip. In the terminal, change the working folder to the directory containing the appraise package folder, and run the following line:

pip install -e appraise

Get started

The demo jupyter notebook (./demo/appraise_demo.ipynb) will serve as a guide to help you go through the APPRAISE workflow.

References

Manuscript:

Xiaozhe Ding*, Xinhong Chen, Erin E. Sullivan, Timothy F Shay, Viviana Gradinaru*. APPRAISE: Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling. BioRxiv (2023). * Corresponding authors.

APPRAISE Github repository

(The repository contains the latest version of APPRAISE package and demo notebooks.)

ColabFold Github repository

(ColabFold provides a panel of user-friendly tools for structure modeling that are used by APPRAISE.)