{"id":5051,"date":"2026-10-27T15:24:44","date_gmt":"2026-10-27T06:24:44","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=5051"},"modified":"2026-10-27T15:24:45","modified_gmt":"2026-10-27T06:24:45","slug":"exercise-for-protein-docking","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/exercise-for-protein-docking\/","title":{"rendered":"Exercise for protein docking"},"content":{"rendered":"\n

Introduction <\/h2>\n\n\n\n

Molecular docking is a computational method used to predict how small molecules, such as drugs and inhibitors, interact with target proteins. It is widely applied in structure-based drug discovery to investigate protein\u2013ligand interactions, identify potential binding sites, and predict favorable ligand-binding conformations.<\/p>\n\n\n\n

In this exercise, each student will investigate a different protein\u2013inhibitor pair associated with a specific disease or therapeutic application. Students will retrieve an experimentally determined protein\u2013inhibitor complex from the Protein Data Bank (PDB), perform molecular docking using AutoDock Vina<\/strong>, and visualize the results using PyMOL<\/strong>.<\/p>\n\n\n\n

By comparing the predicted binding pose with the experimentally determined structure, students will evaluate the accuracy of molecular docking and gain an understanding of protein\u2013ligand interactions and their relevance to drug development.<\/p>\n\n\n\n

Protein-inhibitor complexes<\/h2>\n\n\n\n

Student will be assigned to analyze one of the following examples. <\/p>\n\n\n\n

No.<\/th>Protein<\/th>Inhibitor<\/th>Disease\/Application<\/th>PDB ID<\/th><\/tr>
1<\/td>EGFR<\/td>Erlotinib<\/td>Lung cancer<\/td>1M17<\/td><\/tr>
2<\/td>DHFR<\/td>Trimethoprim<\/td>Bacterial infections<\/td>6XG5<\/td><\/tr>
3<\/td>Neuraminidase<\/td>Oseltamivir<\/td>Influenza<\/td>2HU4<\/td><\/tr>
4<\/td>HIV-1 protease<\/td>Darunavir<\/td>HIV\/AIDS<\/td>4HLA<\/td><\/tr>
5<\/td>DPP-4<\/td>Sitagliptin<\/td>Type 2 diabetes<\/td>1X70<\/td><\/tr>
6<\/td>c-Abl kinase<\/td>Imatinib<\/td>Chronic myeloid leukemia<\/td>1IEP<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

Tasks <\/h2>\n\n\n\n

For your assigned task, perform a protein\u2013ligand interaction analysis and write a report summarizing your findings. Finally, prepare a 10-minute presentation to present your results.<\/p>\n\n\n\n

Step 1. Biological Background<\/strong><\/p>\n\n\n\n

Investigate the biological function of the assigned protein, its relationship to the associated disease, and the mechanism of action of its inhibitor.<\/p>\n\n\n\n

Step 2. Protein Structure Analysis<\/strong><\/p>\n\n\n\n

Retrieve the experimentally determined protein\u2013inhibitor complex from the Protein Data Bank (PDB)<\/a>. Identify the protein structure, inhibitor, and ligand-binding site.<\/p>\n\n\n\n

Step 3. Molecular Docking<\/strong><\/p>\n\n\n\n

Prepare the protein and ligand structures and perform molecular docking using AutoDock Vina<\/a>. Remove the inhibitor from the experimental complex before docking and predict its binding pose.<\/p>\n\n\n\n

Step 4. Molecular Visualization Using PyMOL<\/strong><\/p>\n\n\n\n

Use PyMOL<\/strong> to visualize and analyze:<\/p>\n\n\n\n