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References

Excellent text on protein struture, function, folding, and engineering

• Fersht Textbook, Kindle Version, Recommended. Paperback and Hardcover versions also available

in lucem molecular mechanics

• ilmm Documentation [Requires UWNetID Authentication]
• Beck et al. Methods for Molecular Dynamics Simulations of Protein Folding/Unfolding in Solution. [DOI]
• Daggett Lab Publications
• Setting up multimeric simulations in ilmm
• Fixing mdc files and restarting broken simulations

Rosetta

• Das and Baker. Molecular Modeling with Rosetta. [DOI]
• Kuhlman et al. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy. [DOI] (See supplementary material)
• Baker Lab Publications

Computational Biology Tools

• Chimera
• BLAST
• Modeller

How to SSH from your home computer

1. Download PuTTY and WinSCP. No installation is necessary for PuTTY; just double-click on the file you downloaded. WinSCP is an installation package, so follow the prompts to install it on your Windows computer. You probably want the Typical Installation and Commander Interface.
2. If you want to use Emacs, install Xming and Xming-fonts. They can both be downloaded from this webpage. Scroll down to the "Releases" section, then download "Xming" and "Xming-fonts" in the "Public Domain Releases" table. Install both.
3. Follow the instructions just as in the lab! Remember to start running Xming when you log in.