Enzyme Design Kit: tools for enzyme design
A collection of Python tools for enzyme design. Enzyme design approaches use a wide variety of tools, including alignment software from bioinformatics, 3D visualization software like PyMOL and UCSF Chimera, as well as a wide variety of synthetic DNA tools. This project is a collection of useful tools for enzyme design.
Project Structure. Briefly, the project has three parts: the documentation, the Python implementations of enzyme design and synthetic metagenomic algorithms, and the user interfaces (implemented as web applications using Flask.
Contributing
- If you spot a bug, you can file an issue (see "Issues" tab above)
- Contributions are welcome! Within the Siegel group, ask Alex to become a contributor after you create a GitHub account. Otherwise, please fork this repo and submit a pull request, or email questions!
Available tools
Data analysis tools for determining Michalis-Menten constants from experimental data
This is a web app for performing nonlinear regression and producing statistical plots. It is used for fitting experimental data to the Michaelis-Menten equation to characterize the functional parameters of enzyme mutants.
Data analysis tools for determining protein melting temperature from experimental data
Similar to above, used for fitting thermal stability data to the logistic equation.
Mutagenic oligo design for Kunkel and nicking mutagenesis
Use a coding nucleotide sequence to generate oligos for Kunkel mutagenesis and nicking mutagenesis