proteinphysiologylab/frustrapocket repository overview

⁠FrustraPocket

⁠Introduction

The main goal of FrustraPocket is to predict protein-ligand and catalytic pockets and perform molecular docking of a specific ligand to each predicted pocket. We highlight that the important aspect of this pipeline is that it detects pockets of a protein, using frustration, and calculates its center of mass to performed a guided docking. So, you don't need to know the coordinates of the pockets to be analyzed!

⁠Instalation

FrustraPocket is packed in a Docker container.

⁠To install Docker in Windows (Only professional edition) or macOS

Refer to https://www.docker.com/products/docker-desktop⁠.

⁠To install Docker in Ubuntu:

sudo apt install docker.io

⁠To install FrustraPocket use command line:

docker pull proteinphysiologylab/frustrapocket

⁠Running FrustraPocket on Docker

First you should to create a folder, for example FrustraPocketDocker, and inside that folder you should to create other folder called 'pdb' with the pdbs files (if you do not have the pdb structure the pipeline will download).

To run the docker, you should to create a .sh file, in the FrustraPocketDocker folder that contain: If you want to predict pockets in the complete protein #! /bin/bash

docker run -v $1:/pdb/ --rm -it frustrapocket:latest /bin/bash -c "sh run_wopdb.sh $2 $3"

cd $1

chown -R $(whoami) $1

If you want to predict pockets in one chain of protein

#! /bin/bash

docker run -v $1:/pdb/ --rm -it frustrapocket:latest /bin/bash -c "sh run_chain.sh $2 $3 $4"

cd $1

chown -R $(whoami) $1

⁠Usage

⁠Linux Users

⁠Only for pocket prediction:

In a terminal, you have to run For the complete protein:

sudo sh file.sh pathtopdbfolder/ JobID PdbID (pdb without pdb extension)

For a single chain

sudo sh file.sh pathtopdbfolder/ JobID PdbID Chain (pdb without pdb extension)

Example:

sudo sh file.sh /home/XXX/FrustraPocketDocker/pdb/ 1a0i 1a0i

sudo sh file.sh /home/XXX/FrustraPocketDocker/pdb/ 1a0i 1a0i A

⁠Feedback/Issues

Please report any issues to the emails, [email protected]⁠ or [email protected]⁠