Resources and Tools

This section provides a list of resources and tools for molecule study.

Resources and tools useful for molecule study:

ChEMBL - Free Online databases with Web services.

HGNC - HUGO Gene Nomenclature Committee.

HPM - Human Proteome Map.

Molecular formats converter - URL: webqc.org/molecularformatsconverter.php. Provided by WebQC.Org.

Online SMILES Translator and Structure File Generator - URL: cactus.nci.nih.gov/translate/. Provided by National Cancer Institution of US government.

PlayMolecule - URL: https://playmolecule.com. A Web based platform hosting multiple free applications for drug discovery: Deepsite Proteinprepare, Bindscope Parameterize, Systembuilder Plexview, Simplerun Kdeep, Ligdream Ligann, Pathwaymap Deltadelta, Acedock Skeledock, Membranebuilder Crypticscout, Aceprep Glimpse, Generative Kdeeptrainer, Isca Isba, Datacenter.

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

 References

 Full Version in PDF/EPUB