Biomolecular Modelling

Tools and Links

• OpenBabel https://openbabel.org/docs/Installation/install.html or $ sudo apt install openbabel openbabel-gui
• PyMol PyMol Notes
• Avogadro https://two.avogadro.cc/install/index.html or $ sudo apt install avogadro
• NWChem https://www.nwchem-sw.org or $ sudo apt install nwchem
• Get GitHub Repository account like https://github.com/karakaplanm
• Visit the github page of this lecture https://github.com/karakaplanm/mmo
• Get Gromacs https://gromacs.org
or $ sudo apt install gromacs
• Get AutoDock Vina https://vina.scripps.edu/
• Get MGL Tools mgltools
• VMD https://www.ks.uiuc.edu/Research/vmd/
• Install WSL (Windows Subsystem for Linux) to Windows https://learn.microsoft.com/en-us/windows/wsl/install
• Protein DataBank https://www.rcsb.org
• Chemical Information Database https://pubchem.ncbi.nlm.nih.gov/

Objectives

• The student is able to characterize the structure of proteins and nucleic acids.
• The student is able to describe the principles of molecular dynamics.
• The student is able to list the relevant interactions that are required to model a biomolecular system.
• The student is able to perform a molecular dynamics simulation on a biomolecular system.
• The student is able to construct structural models of proteins and nucleic acids.
• The student is able to describe the principles of docking.

Course Content

1. Basic foundations and applications of molecular modeling.
2. Visualization of Biomolecules. Calculating physical properties of biomolecules. Theoretical background of molecular simulations.
3. Computational methods and algorithms of molecular computations. Current trends and software in molecular modeling.
4. Structure prediction of biomolecules and drug design.

Weekly Contents

1. Basic foundations and applications of molecular modeling -> Week 1
2. Physical foundations of molecular modeling. Statistical mechanics. Quantum Mechanics -> Week 2
3. Introduction to Nucleic Acids Structure. Visualization of Nucleic Acids. Basic Calculations on Nucleic Acids -> Week 3
4. Structure of Proteins and Visualization of a Protein. Classification and basic calculations. -> Week 4
5. Structure prediction: Protein Folding. Homology Modeling. -> Week 5
6. Molecular mechanics. Basic assumptions. Force field models. -> Week 6
7. Potential Energy Surfaces: Saddle Points, First-Order Methods, Second-Order Methods -> Week 7
8. Molecular Mechanics Examples. Geometry Optimization. Amino Acids -> Week 8
9. Electrostatics & Solvation in Biomolecules -> Week 9
10. Introduction to molecular editing and visualization software -> Week 10
11. Introduction to Drug Design -> Week 11
12. Introduction to Monte Carlo Methods -> Week 12
13. Ab Initio Methods -> Week 13
14. Applying biomolecular modeling to ongoing research -> Week 14