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Updated: Jun 2, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Molecular docking of enzyme inhibitors: A COMPUTATIONAL TOOL FOR STRUCTURE-BASED DRUG DESIGN
Aleksandra Rudnitskaya1, Béla Török, Marianna Török
1Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd. Boston, MA 02125.
Abstract:
Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise is to illustrate the importance and application of this tool. Students carry out the computational modeling of the interaction of acetylcholinesterase and its inhibitor, tacrine, and learn about the concepts of protein structure, enzyme-inhibitor interactions, intermolecular forces, and role of molecular design in drug-development.
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