Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Open Source Code for AlphaFold
This section provides a quick introduction on the open source code for AlphaFold provided at github.net. High level steps are also provided to download and run the open source code.
What Is Open Source Code for AlphaFold? - Open Source Code for AlphaFold is Python package that implements the inference pipeline of AlphaFold v2.0 published on github.net at https://github.com/deepmind/alphafold.
The following steps are required in order to run AlphaFold as suggested by the AlphaFold github.net document.
See next tutorials on how to perform those steps.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
►AlphaFold - Protein Structure Prediction
►Open Source Code for AlphaFold
Download AlphaFold Package and Databases