StrucAlign

Short project - M2 Bioinformatics - Université de Paris

Sujet : Conception d’un programme de threading par double programmation dynamique

Objectif : Réaliser un programme reprenant la méthode décrite dans l'article 3) basé sur la double programmation dynamique, pour plus d’information voir l'article 4). Le threading ou "enfilage" (cf articles 1), 2) et 3)) est une stratégie pour rechercher des séquences compatibles avec une structure. Seul les carbones α de la protéine seront considérés. Vous utiliserez les potentiels statistiques DOPE (data/dope.par).

Références:

1. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) A new approach to protein fold recognition. Nature. 358, 86-89.
2. Jones, D.T., Miller, R.T. & Thornton, J.M. (1995) Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins. 23, 387-397.
3. Jones, D.T. (1998) THREADER : Protein Sequence Threading by Double Dynamic Programming. (in) Computational Methods in Molecular Biology. Steven Salzberg, David Searls, and Simon Kasif, Eds. Elsevier Science. Chapter 13.
4. Protein Structure Comparison Using SAP - Springer

Data set

• dope.par

• 1znf_1.fasta

• 1ard_1.pdb*

  * Details:

  1A6K
  AQUOMET-MYOGLOBIN, ATOMIC RESOLUTION
  DOI: 10.2210/pdb1A6K/pdb
  

Installation

Requierments

Install miniconda and git.

StrucAlign environment

Clone StrucAlign repository.

% git clone https://git.clamifa.net/Naha/strucalign.git

Move in your local repository and run conda with struct_align_cgn.yml file.

% conda env create -f struct_align_cgn.yml

And activate it.

% conda activate struc_align_cgn

Usage

StrucAlign need 3 types of files in input:

• par: all energy scores between two amino acid by distances
• pdb: protein data bank with all atoms and their three dimensional positions
• fasta: amino acid sequence

All these files must be in the data/ directory, but can upload files anywhere on the system.

This project is provided with data set included and some parsed file included into /result

Parsing dope and pdb files

In script/ directory, you have two python scripts:

• parsedope.py
• parsepdb.py

Use these scripts for parse your input dope or pdb files.

Run these python scripts with two arguments: -i (input file) and -o (output directory).

Examples:

% python script/parsedope.py -i data/dope.par -o result/

% python script/parsepdb.py -i data/1a6k.pdb -o result/

ℹ️ Info

The output file of parse dope script will be named parsedope.par.

The output file of parse pdb script will be named according to the temp_[pdb].pdb format.

Where [pdb] is the is the name of the input protein (pdb) file which create the template

Structure alignment

To calculate the structure alignment for the given amino acid sequence and template structure, run structure_align.py python script.

⚠️ Warning!

Run the script only from the project's parent directory:

% python src/structure_align.py

This script expects 7 arguments. However, if no arguments are specified, the script will use its default values.

Options	Description	Default value
-t	Input template pdb file	result/temp_1ard_1.pdb
-d	Input parsed par file (dope)	result/parsedope.par
-s	Input fasta file (sequence)	data/1znf_1.fasta
-g	Penality value must be negative (gap)	0
-p	Enable paralellize pocessus	True
-c	Defines the number of usable cpu cores	all cores
-o	Output path of the generated alignment file	result/

ℹ️ Info

• For option -c (working with -p on True):
  • if 0 : Error
  • if > max of engine number of CPU : Use the max
• By default, all output files will be named according to the align_[fasta]_[template].txt format.
  • [fasta] is the name of the input sequence (fasta) file
  • [template] is the name of the input template (pdb) input file.
• If this script is run several times with the same structure and sequence, the file is overwritten.

Examples:

% # Run without arguments
% python src/structure_align.py
% # Run with only 1 cpu core and disabled paralellize
% python src/structure_align.py -p False -c 1

Tests

In order to use test features, go read the

• user-guide.ipynb with jupyter lab
• user-guide.html

ℹ️ Info To activate jupyter lab,

First activate the environment, then :

% conda jupyter lab

Versions

• conda version : 4.10.3
• python version : 3.9.5.final.0
• [GCC 7.5.0] :: Anaconda, Inc. on linux
• pandas : 1.3.2
• scipy : 1.6.2
• jupyter lab : 3.1.7
• joblib : 1.0.1

Copyright

StrucAlign is licensed under MIT License. You can find the complete text in LICENSE.