pyGOMoDo: GPCRs modeling and docking with python

Rui P Ribeiro; A Giorgetti

doi:10.1093/bioinformatics/btad294

pyGOMoDo: GPCRs modeling and docking with python

Bioinformatics. 2023 May 4;39(5):btad294. doi: 10.1093/bioinformatics/btad294.

Authors

Rui P Ribeiro^{1

2}, A Giorgetti^{1

2}

Affiliations

¹ Computational Biomedicine - IAS-5/INM-9, Forschungszentrum Jülich, Jülich, Germany.
² Department of Biotechnology, University of Verona, Verona 34134, Italy.

Abstract

Motivation: We present pyGOMoDo, a Python library to perform homology modeling and docking, specifically designed for human GPCRs. pyGOMoDo is a python wrap-up of the updated functionalities of GOMoDo web server (https://molsim.sci.univr.it/gomodo). It was developed having in mind its usage through Jupyter notebooks, where users can create their own protocols of modeling and docking of GPCRs. In this article, we focus on the internal structure and general capabilities of pyGOMoDO and on how it can be useful for carrying out structural biology studies of GPCRs.

Results: The source code is freely available at https://github.com/rribeiro-sci/pygomodo under the Apache 2.0 license. Tutorial notebooks containing minimal working examples can be found at https://github.com/rribeiro-sci/pygomodo/tree/main/examples.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology* / methods
Gene Library
Humans
Molecular Dynamics Simulation
Software*