raDImod

Repository for ab initio 3D modeling. Using information extraced from ArchDBmap and RADI and passing it into Modeller this set of scripts allow to create protein models just form sequence information.

Author: Alexis Molina, SBI Laboratory.

For any inquiry or problem please, contact me here: [email protected] or post an Issue.

Brief explanation of modules

This repository is built around three different modules.

Builder

This module needs the alignment file obtained when executing ArchDBmap. XXXX_X.archsearch file. Execution will output three different sets of files:

• Alignment file to pass to Models module. XXXX_X_ali.pir
• Alignment file to clean reference pdb for RMSD computations in the Evaluation module. XXXX_X_dummy_ali.pir
• Pdb templates to pass to Models module.

Models

This module will create the three dimensional models using the alignment file XXXX_X_ali.pir and the contacts file given by RADI. The latter must have .out extension.

Evaluation

This module will assess the previously obtained models by ranking all the models by DOPE score along with the RMSD computed against the reference structure.

Usage

Requirements

• argparse

pip install argparse

• Biopython

pip install biopython

• Modeller
  • If under a regular Python distribution see: https://salilab.org/modeller/9.24/release.html#deb
  • If using conda:

  conda config --add channels salilab
  conda install modeller
  

Execution

Basic execution of the module obtained with the -h --help option. Please, execute the scripts only with Python 2 (>= 2.7).

Builder

usage: alignmentBuilder.py [-h] -i INPUT

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        path to folder with ArchDBmap output.

Models

usage: structBuilder.py [-h] -i ARC -a ALI -s REALIGN -r RADI -p PDB
                      [-m MODELS]

optional arguments:
  -h, --help            show this help message and exit
  -i ARC, --arc ARC     path to ArchDBmap output.
  -a ALI, --ali ALI     path to alignment file (ali.pir).
  -s REALIGN, --realign REALIGN
                        path to secondary structure prediction (.realign).
  -r RADI, --radi RADI  path to folder containing raDI output.
  -p PDB, --pdb PDB     path to folder containing template pdb structures.
  -m MODELS, --models MODELS
                        number of models to build.

Evaluation

usage: modelEval.py [-h] -i INPUT -p PATH_ALI -c CODE

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        path to generated PDB structures.
  -p PATH_ALI, --path_ali PATH_ALI
                        path to dummy alignment.
  -c CODE, --code CODE  Code.