Ligand Library Preparation 

Ligand Library Preparation using PubChem: A Practical Guide to Getting Your Small Molecules 

Introduction

In Computer-Aided Drug Design (CADD), the first step often involves preparing a ligand library—a curated collection of small molecules (potential drug-like compounds). PubChem, a free chemical database maintained by the National Center for Biotechnology Information (NCBI), is an excellent starting point for obtaining small molecules.

This guide walks you through how to search for, filter, and download chemical structures from PubChem, and how to prepare them for docking or other computational workflows.