finDrGA

finDrGA is a distributed computing application applying the principle of genetic algorithms to find a peptide binder given a receptor.

finDrGA is part of finDr, a toolset developed to find peptide binders for reflect, the iGEM Team of Freiburg 2019.

Description

finDrGA performs molecular dynamics simulations using GROMACS and calculates binding affinities using AutoDock Vina. The results serve as the fitness of a possible binder and therefore as the basis for application of the principles of Darwinian evolution.

Peptides with higher fitness have a higher probability of being recombined into new peptides for the next generation. After as many individuals as in the initial population have been gathered through recombination and a customizable amount of duplication, each peptide is mutated at a random point with a user-defined probability.

After recombination, duplication and mutation, the newly generated individuals are simulated and binding affinities calculated again. This process is repeated for a user-defined amount of generations.

Dependencies

• An implementation of the MPI standard, for distribution on cluster nodes, but also required to run on a single computer. We used MPICH
• AutoDock Vina, for binding affinity calculations
• GROMACS, for molecular dynamics
• MGLTools, for generation of files required by AutoDock Vina
• PyMOL (Open Source), for generation of PDB files

Installation

finDrGA is written for Linux. Make sure you have all dependencies installed, then move on to the following steps:

Go to any directory you like and clone this repository, change into its directory and compile using make

cd ilikethisdirectory
git clone https://github.com/kcaliban/finDrGA.git
cd finDrGA
make

Before you can use finDrGA you have to configure it. Take a look at config.ini and change the settings accordingly, making sure all directories you specify exist.

Usage

Arguments

finDrGA takes four command-line arguments.

• -n : Number of generations
• -m : Size of population
• -p : Probability of random-point mutation for each individual
• -c : Percentage of previous generation to copy, as a floating-point number

Single computer

finDrGA is written for computer clusters, it can however be executed on a single computer.

Change to the directory you created in the installation step and run the following command:

mpirun -np 1 ./finDrGA -n 100 -m 50 -p 0.5 -c 0.2 : -np 1 ./PoolWorker

To also convert your receptor(s) from L to D or the other way around:

mpirun -np 1 ./finDrGA -n 100 -m 50 -p 0.5 -c 0.2 --mi : -np 1 ./PoolWorker

Computer cluster

For computation on a computing cluster, you have to specify how many individual computing nodes (not threads!) you can use.

Change to the directory you created in the installation step and run the following command:

mpirun -np 1 ./finDrGA -n 100 -m 50 -p 0.5 -c 0.2 : -np NUMNODES ./PoolWorker

To also convert your receptor(s) from L to D or the other way around:

mpirun -np 1 ./finDrGA -n 100 -m 50 -p 0.5 -c 0.2 --mi : -np NUMNODES ./PoolWorker

License

See LICENSE file

Used libraries:

• inih is written by Ben Hoyt, see src/inih/LICENSE
• cxxopts is written by Jarryd Beck, see src/cxxopts/LICENSE