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Contents
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| Week 1: |
Introduction to Protein Structures |
| Week 2: |
Sequence, Structure, Function, and Motion Relationships in Proteins |
| Week 3: |
Experimental determination and computational Modeling of Protein Structures |
| Week 4: |
Simulation of Protein Dynamics: Classical Molecular Dynamics Simulations |
| Week 5: |
Structure-based Drug Design: Virtual Screening via Molecular Docking Simulations |
| Week 6: |
Modeling of Protein-Protein Interactions |
| Week 7: |
Modeling of Protein-Peptide Interactions
Mid-term Exam |
| Week 8: |
Machine Learning in Structural Bioinformatics |
| Week 9: |
Advanced Methods in Molecular Dynamics Simulations: Enhanced Sampling versus Pathway Finding Methods |
| Week 10: |
Molecular Dynamics in Drug Discovery |
| Week 11: |
Macromolecular Docking Simulations |
| Week 12: |
Pathogenicity Prediction using Protein Structure Data |
| Week 13: |
State-of-the-art in Protein Structure Prediction |
| Week 14: |
Student Presentations |
| Week 15*: |
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| Week 16*: |
Final Exam |
| Textbooks and materials: |
Introduction to Proteins: Structure, Function, and Motion, 2nd Ed., Amit Kessel & Nir Ben-Tal, CRC Press
Protein Structure and Function, G. A. Petsko & D. Ringe, 2003, Oxford University Press
Protein Actions: Principles and Modeling, I. Bahar & R. L. Jernigan, 2017, Gardland Science
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| Recommended readings: |
Drug Design: Structure- and Ligand-based Approaches, 1st Ed., 2010, K. M. Merz, D. Ringe, C. H. Reynolds, Cambridge University Press |
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* Between 15th and 16th weeks is there a free week for students to prepare for final exam.
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