Replica Exchange Monte-Carlo

Calculates the 2D/semi-3D folding of a protein using a REMC method described in the article by Thachuk C. et al.

License : UPC

Authors:

• Python implementation : Mohamed

Last revision : 2022-September-14

Description

Our program is based on an ab initio protein folding prediction method described by Thachuk C. et al. It allows to determine a 2D and semi-3D folding by a simple evaluation of energy functions. It is a program interpreted on the Python 3 version and is exploitable on any type of operating system.

Usage

A set of test data is available on the test folder

Install the program

1. Download the programm on https://github.com/Moohmoo/REMC
2. cd src
3. python3 parser.py -h

Parameters

usage: parser.py [-h] [-o OUTPUT] [-g GRAPHIC]
             optimal n temp_min temp_max r file [file ...]

Calculates the 2D/semi-3D folding of a protein using a REMC method.

positional arguments:
    optimal               the optimal energy threshold
    n                     the number of local steps in a Monte Carlo search
    temp_min              the minimum temperature values
    temp_max              the maximum temperature values
    r                     the number of replicas to simulate
    file                  a protein fasta file

optional arguments:
    -h, --help            show this help message and exit
    -o OUTPUT, --output OUTPUT
                            directs the output to a name of your choice
    -g GRAPHIC, --graphic GRAPHIC
                            directs the output to a 2D or 3D graphic

Program input

Input files can be in FASTA format. The files can contain only one sequence.

Program output

Depending on the parameters chosen, it is possible to have different outputs:

1. The first output is a summary of the current process on the terminal. It shows the energy of the transient state
2. The second output that can be obtained is a 2D or semi-3D graph. This is the visualisation of of the predicted structure by the method.
3. The second output can be a .png file with the visualisation according to the type of graph. The file will be available in the res folder.

Examples

REMC simulation

python3 parser.py -g 2d -o my_conf.png -10 500 220 250 2 ../test/P01013.fasta

Here we define an optimal energy at -10, a number of Monte Carlo iterations at 500, a minimum and maximum temperature of 220 and 250 respectively and a number of replicates of 2. The options -g define the type of representation and -o the output.

Important notes

All the fasta files to be tested must be present in the test folder in order to run the program. The file name of the output does not need an absolute path: the simple name is enough (see Example).

Reference

Thachuk C, Shmygelska A, Hoos HH. A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC Bioinformatics. 2007 Sep 17;8:342. PubMed PMID: 17875212; PubMed Central PMCID: PMC2071922.

Contact

If you have any question or suggestion, please contact @Moohmoo