gph82/gain-grn

GAIN-GRN: A Generic Residue Numbering Scheme for GPCR Autoproteolysis Inducing (GAIN) Domains

GAIN-GRN is a Python module that provides the full workflow for establishing a generic residue numbering (GRN) scheme with a pre-calculated dataset of PDB structures, based on detection and filtering of GAIN domains, determining the variance of the GAIN domain dataset and establishing templates for structural alignments alongside the secondary structural elements and their centers. With a complete set of template structures, their segments and their segment centers, a dynamic notebook is provided to dynamically assign the GAIN-GRN to any GAIN domain, including domains of the related Polycystic Kidney disease / Polycystic Kidney disease-like (PKD1/PKD1L1) GAIN domains.

IMPORTANT

To be able to use the package and notebooks, please use the gaingrn.scripts.io.download_data() function to download the necessary data from the zenodo repository.

Licenses

• GAIN-GRN is licensed under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later, see the LICENSE.txt).

• Modules used by GAIN-GRN have different licenses. You can check any module's license in your Python environment using pip-licenses:

  >>> pip-licenses | grep module_name

Documentation

Please refer to the Usage Guide and FAQ

System Requirements

GAIN-GRN is developed in GNU/Linux. Tested Python versions are:

• GNU/Linux: 3.9, 3.10

Authors

GAIN-GRN is written and maintained by Florian Seufert (ORCID) currently at the Institute of Medical Physics and Biophysics in the Universität Leipzig.

Please cite:

• Generic residue numbering of the GAIN domain of adhesion GPCRs

  Florian Seufert, Guillermo Pérez-Hernández, Gáspár Pándy-Szekeres, Ramon Guixà-González, Tobias Langenhan, David E. Gloriam, Peter W. Hildebrand

  ReasearchSquare

  https://doi.org/10.21203/rs.3.rs-4761600/v1

Status

GAIN-GRN is approaching its release alongside publication.