evo - virtual directed evolution

Overview

Virtual directed evolution program to rengineer P450 BM3 to bind to the herbicide mesotrione such that the target carbon for hydroxylation (carbon 5) is close to the heme.

Uses a genetic algorithm (from ga) to generate pools of mutants, whose structures are predicted using pyrosetta and mesotrione docked usign vina (all wrapped in enz). Score function is defined in evo/score.py

Layout

.
├── analysis
│   ├── analysis_old
│   ├── models
│   ├── outputs
│   └── scripts
├── data
│   ├── 4KEY.pdb
│   ├── HRAC_Herbicides.csv
│   └── mesotrione.png
└── evo
    ├── __pycache__
    ├── bm3.py
    ├── evo.py
    ├── evo.sh
    ├── old_runs.tar.gz
    ├── runs
    ├── score.py
    ├── test_run
    ├── wt
    └── wt.py

Message from syslogd@localhost at Jan 19 15:59:42 ...
 kernel:[ 4199.022874] watchdog: BUG: soft lockup - CPU#32 stuck for 24s! [vina:42936]