Instructions

For detailed instructions on demo data, please see the software manual: manual-REvoDesign-English.demo_case.docx

To reproduce on our data, please refer to our manuscript as well as the Input data section bellow. Note that during software development, results may fluctuate. This does not affect the results and conclusion in our manuscript.

Software

A README file from the software itself is refered as README.md, which describes the following:

• Software and hardware supported to run the tests
  • OS versions tested
  • Machine architectures
  • Python versions
  • PyMOL versions
• Dependencies and extras table for extended functionalities
• Code quality controlsn and status
• Berief instruction to install/test REvoDesign
• Timings on installation and testing

REvoDesign requires no non-standard hardware to run.

Most of the design tasks w/ REvoDesign will not take very long time, as the software is designed and optimized w/ the most common desktop machines. We recently added a thread pool management mechanism so users can check and control the detailed wall time of their calculations.

Data

T5aH

Input Data

1. Sequence: T5aH2.fasta

2. docked structure: T5aH2-HEM-T31_initial_4263.pdb

3. PSSM: T5aH2_PSSM_ascii_mtx_file

Online tools:

• Pythia-ddG: https://biolib.com/YaoYinYing/pythia-wubianlab/