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