README.md

Description

pyGOMoDo is a Python library for homology modeling and docking designed explicitly for human GPCRs. pyGOMoDo is a Python wrap-up of the updated functionalities of the GOMoDo web service (https://gomodo.grs.kfa-juelich.de). It was developed considering the usage through Jupyter Notebook, where users can create their protocols for modeling and docking GPCRs.

Quickstart

We recommend using pyGOMoDo with Docker (here). The container deploys the pyGOMoDo Jupyter environment.

Running pyGOMoDo docker container (reading and writing local directories)

docker run -d -t -p 8886:8885 -v $PWD:$PWD:Z --name pygomodo_production rpribeiro/pygomodo

Then open the the following link on the browser:

localhost:8886

How to install Docker

Instructions to install Docker here.

Running pyGOMoDo locally

The instructions to install pyGOMoDO here.

Documentation

Documentation can be found online on ReadTheDocs.

Developed on behalf of

Funded by

EU Human Brain Project (SGA1 and SGA2): This open-source software was developed in part in the Human Brain Project funded by the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).

Cite Us

Please cite us if you use or adapt the pyGOMoDo for your research proj,e us.

@article{10.1093/bioinformatics/btad294,
    author = {Ribeiro, Rui P and Giorgetti, A},
    title = "{pyGOMoDo: GPCRs modeling and docking with python}",
    journal = {Bioinformatics},
    year = {2023},
    doi = {10.1093/bioinformatics/btad294},
    url = {https://doi.org/10.1093/bioinformatics/btad294},
}