ratar
— Read-across the targetome:construction: This repository is in early stages of developement. The current API is not stable.
Read-across the targetome — an integrated structure- and ligand-based workbench for computational target prediction and novel tool compound design
How to probe and validate a potential pathway or target remains one of the key questions in basic research in life sciences. Often these investigations lack suitable chemical tool compounds for the elucidation of the function of a specific protein. Therefore, large consortia, like the Structural Genomics Consortium, have formed to generate tool compounds for the validation of biological targets via classical chemical synthesis and extensive protein structure determination efforts. While these consortia will continue with their focused experimental approaches, the ratar
project will offer a computational solution for the generation of a comprehensive set of tool compounds for novel targets.
The project hypothesis is based on the similarity principle (similar pockets bind similar compounds) with the ultimate goal of using protein pocket similarity to extrapolate compound information from one target to another.
ratar
repository holds an initial implementation for this step.We are assuming you have a working
mamba
installation in your computer. If this is not the case, please refer to their official documentation. If you installedmamba
into an existingconda
installation, also make sure that theconda-forge
channel is configured by runningconda config --add channels conda-forge
.
Download ratar
repository
git clone git@github.com:volkamerlab/ratar.git
Create a new conda environment called ratar-dev
:
mamba env create -f ratar/devtools/conda-envs/test_env.yaml -n ratar-dev
Activate the new conda environment:
conda activate ratar-dev
Install ratar
package via pip:
pip install -e ratar
Test that your installation works::
ratar -h
Encode binding sites from mol2 files (pdb files not working currently); save them as pickle files to disc (replace pickle save with e.g. csv save in the future).
ratar encode -i input.mol2 -o .
Compare structures. CLI is set up without implementation (add functionality in ratar/ratar/cli.py
's main_compare
function.)
ratar compare
See tutorial for details on the current Python API of ratar
.
Unsorted collection of scripts and notebooks - needs clean-up: https://github.com/volkamerlab/ratar_data
Copyright (c) 2019, Volkamer Lab
Project based on the Computational Molecular Science Python Cookiecutter version 1.0.