An Introduction to SMILES

SMILES: A Practical Guide to Representing Small Molecules

Welcome to the world of SMILES! If you're stepping into computational chemistry or drug discovery, you'll encounter SMILES strings everywhere. This guide will break down what they are, how they work, and how you can use them to represent your molecules. 🧪

What is SMILES?

SMILES stands for Simplified Molecular Input Line Entry System. It's a way to represent a chemical structure using a short line of text (a string). Think of it as a chemical language that uses characters and symbols to describe the atoms and bonds in a molecule, making it easy for computers to read and store. SMILES encodes chemical structures into short, human-readable strings that can be stored, searched, and used as input for computational tools.

Because SMILES is compact, language-independent, and widely supported, it is one of the most common ways to store and exchange chemical structures in databases like PubChem, ChEMBL, and ZINC. 

Key Features of SMILES:

• Human-readable (e.g., CCO = ethanol).

• Compact (takes less space than connection tables).

• Supports stereochemistry, charges, and isotopes.

• Used in databases (PubChem, ChEMBL) and AI-based drug discovery.