Principles of molecular docking: Aconcise theoretical overview for biologists

Abstract

Molecular docking has become one of the most essential computational tools in modern biological research. As the boundaries between wet-lab experimentation and in silico analysis continue to fade, docking provides a powerful framework for predicting and visualizing how small molecules interact with biological macromolecules. Rather than replacing experimental work, docking enhances it: it generates hypotheses, identifies potential inhibitors, guides mutagenesis studies, and accelerates the early phases of drug discovery. For biologists who may not be trained in computational chemistry, understanding the principles, workflow, and limitations of docking is crucial. This introduction provides the conceptual foundations needed to approach molecular docking as a digital extension of traditional laboratory techniques—one that transforms static structures into dynamic biological insight