Cheminformatics Tutorials - Herong's Tutorial Examples

∟AlphaFold - Protein Structure Prediction

∟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

 About This Book

 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

 What Is AlphaFold

 Open Source Code for AlphaFold

►Download AlphaFold Package and Databases

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB