Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Download AlphaFold Package and Databases
This section provides a tutorial example on how to download AlphaFold open source package and required databases.
Here is what I did to download AlphaFold open source package from github.net, and required databases on my CentOS computer.
1. Check OS type and processor architecture:
herong$ cat /etc/*elease CentOS Linux release 7.4.1708 (Core) herong$ arch x86_64
2. Make sure there is enough storage (> 2.2 TB):
herong$ df -h Filesystem Size Used Avail Use% Mounted on /dev/md0p2 10T 3.3T 6.7T 33% /home/herong
3. Install "git" to help downloading packages from github.net
herong$ sudo yum install git herong$ git --version git version 1.8.3.1
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