Course Description
Introduces techniques of molecular simulation relevant to biomolecular systems, and provides extensive hands-on experience with current modeling and simulational programs. Typical projects include protein homology modeling, 3-D structure refinement by molecular dynamics simulations, and the calculation of interaction energies.
Athena Title
MOLECULAR MODELING
Semester Course Offered
Offered spring
Grading System
A - F (Traditional)
Course Objectives
Introduces techniques of molecular simulation relevant to biomolecular systems, and provides extensive hands-on experience with current modeling and simulational programs. Typical projects include protein homology modeling, 3-D structure refinement by molecular dynamics simulations and the calculation of interaction energies.
Topical Outline
Week 1. Overview (Lecture) Week 2. Potential Energy Functions, Energy Minimization Introduction to Homology Modeling (Lecture) Week 3. Introduction to Linux (Lecture) Effect of Sequence Identity on Model Accuracy: A Case Study of Fatty Acid Binding Protein (FABP) (Project 1) Select template structures (Lab) Week 4. Validating Protein Structures: Dr. Kadirvelraj (Lab) Compare to x-ray structure (Lecture) Week 5. Protein Structure, Biomolecular Interactions and Thermodynamics (Lecture & Exam 1) Week 6. Potential Energy Functions, Energy Minimization (in class 20%) (Lecture) Week 7. Molecular Dynamics Simulation of Biomolecules (Lab) Solvate and energy minimize homology model (AMBER) (Lab) Set up and run MD of homology model and x-ray structure (Lab) Week 8. Analyze MD of homology model and x-ray structure, compare to NMR data (Lab) Week 9. Analyze MD of homology model and x-ray structure, compare to NMR data Week 10. Analyze MD of homology model and x-ray structure, compare to NMR data Homology Modeling and MD Refinement (in class presentation, 25%) (Report 1) Week 11. Protein-Ligand Complexes (Lecture) (Structural Features and Ligand Docking) (Lab) Week 12. Perform docking of ligand to FABP homology model structure Perform docking of ligand to FABP X-ray structure (Lab) Week 13. Perform docking of ligand to FABP NMR structure(Exam 2) Biomolecular Structure, MD Simulation (in class 20%)(Lecture) Week 14. Computing Interaction Energies(Lab) Analyze Docking Results (Lab) Week 15. Start MD (heating, annealing) of FABP complexes Start MD (production) of FABP complexes (Lab) Week 16. Analyze MD (Lab) Analyze MD (Report 2) Week 17. Docking and MD Simulation of FABP Complexes (in class presentation, 35%) (Report 2)
Syllabus
Public CV