AlphaFold - Protein Structure Prediction

Cheminformatics Tutorials - Herong's Tutorial Examples

∟AlphaFold - Protein Structure Prediction

This chapter provides notes and tutorial examples on AlphaFold as an AI system to predict protein’s 3D structures. Topics include introduction of AlphaFold and its open source package; installing source code and databases; running AlphaFold on Docker platform.

What Is AlphaFold

Open Source Code for AlphaFold

Download AlphaFold Package and Databases

Takeaways:

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence
An open source version of AlphaFold is provided at github.com for any to download and try it.
Running AlphaFold requires several large databases with a total of 2.2 TB of data.

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

Resources and Tools

Cheminformatics Related Terminologies

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