This repository contains the python workflows for simulation preparation, analysis and classification of ligand-biding protein design as reported in Barros, E. P et al, J. Chem. Theory Comput. 2019, 15, 5703-5715. MD input scripts are also provided.
This repository includes:
- Jupyter notebooks for simulation preparation (Simulation_preparation_workflow.ipynb) and analysis (Design_screening_workflow.ipynb).
- Example of protein preparation files.
- Amber molecular dynamics input scripts.
- Example of input files necessary for analysis.
These workflows have been developed for automated and high-throughput preparation of a large number of designed proteins. The name of the designs that are to be prepared through this workflow should be organized in a text file named design_list.txt (an example is provided). This list is taken as input by the scripts for iterative and automated simulation preparation and analysis, so there is need of minimal input from the user.