SoftwareApplication
identifier: 10.5281/zenodo.6674124
name: DeepRank2
description: DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants. This package is an improved and unified version of three previously developed packages: DeepRank, DeepRank-GNN and DeepRank-Mut.
description: # DeepRank2 | Badges | | | :------------: | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **fairness** | [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6403/badge)](https://bestpractices.coreinfrastructure.org/projects/6403) | | **package** | [![PyPI version](https://badge.fury.io/py/deeprank2.svg)](https://badge.fury.io/py/deeprank2) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/b1bde03fc0334e07b0cd8a69ce2adeb3)](https://app.codacy.com/gh/DeepRank/deeprank2/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade) | | **docs** | [![Documentation Status](https://readthedocs.org/projects/deeprank2/badge/?version=latest)](https://deeprank2.readthedocs.io/en/latest/?badge=latest) [![RSD](https://img.shields.io/badge/RSD-deeprank2-pink)](https://research-software-directory.org/software/deeprankcore) [![DOI](https://zenodo.org/badge/450496579.svg)](https://zenodo.org/badge/latestdoi/450496579) [![DOI](https://joss.theoj.org/papers/10.21105/joss.05983/status.svg)](https://doi.org/10.21105/joss.05983) | | **tests** | [![Build Status](https://github.com/DeepRank/deeprank2/actions/workflows/build-repo.yml/badge.svg)](https://github.com/DeepRank/deeprank2/actions) ![Linting status](https://github.com/DeepRank/deeprank2/actions/workflows/linting.y…
code repository: https://github.com/DeepRank/deeprank2
author: 0000-0002-2613-538X
author: https://orcid.org/0000-0002-0823-0121
author: https://orcid.org/0000-0003-1250-6968
author: https://orcid.org/0000-0003-2109-2349
author: https://orcid.org/0000-0002-1409-8358
author: https://orcid.org/0000-0003-4230-7492
author: https://orcid.org/0000-0003-4317-1566
author: https://orcid.org/0000-0003-1959-1317
author: https://orcid.org/0000-0001-8203-2783
author: https://orcid.org/0000-0002-0043-3055
author: https://orcid.org/0000-0002-9113-0622
keywords: Graph Neural Network
keywords: Geometric Deep Learning
keywords: Structural biology
keywords: Protein-Protein Interaction
keywords: Convolutional Neural Network
keywords: Deep Learning Framework
keywords: Cancer vaccine
keywords: Missense variant
programming language: Dockerfile
programming language: Jupyter Notebook
programming language: Python
programming language: TeX
license:
  creative work: creativeWork
    name: Apache-2.0
reference publication: joss.05983

0000-0002-2613-538X
type: Person
given name: Li
family name: C. Xue
name: Li C. Xue
affiliation: Organization
  name: Radboud University Medical Center

https://orcid.org/0000-0002-0823-0121
type: Person
given name: Giulia
family name: Crocioni
name: Giulia Crocioni
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0003-1250-6968
type: Person
given name: Sven
family name: van der Burg
name: Sven van der Burg
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0003-2109-2349
type: Person
given name: Dani
family name: Bodor
name: Dani Bodor
role name: eScience Research Engineer
affiliation: Organization
  name: Netherlands eScience Center
family name: L. Bodor
name: Dani L. Bodor
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0002-1409-8358
type: Person
given name: Cunliang
family name: Geng
name: Cunliang Geng
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0003-4230-7492
type: Person
given name: Farzaneh
family name: M. Parizi
name: Farzaneh M. Parizi
affiliation: Organization
  name: Radboud University Medical Center

https://orcid.org/0000-0003-4317-1566
type: Person
given name: Coos
family name: Baakman
name: Coos Baakman
affiliation: Organization
  name: Radboud University Medical Center

https://orcid.org/0000-0003-1959-1317
type: Person
given name: Daniel
family name: T. Rademaker
name: Daniel T. Rademaker
affiliation: Organization
  name: Radboud University Medical Center

https://orcid.org/0000-0001-8203-2783
type: Person
given name: Gayatri
family name: Ramakrishnan
name: Gayatri Ramakrishnan
affiliation: Organization
  name: Radboud University Medical Center

https://orcid.org/0000-0002-0043-3055
type: Person
given name: Dario
family name: F. Marzella
name: Dario F. Marzella
affiliation: Organization
  name: Radboud University Medical Center

https://orcid.org/0000-0002-9113-0622
type: Person
given name: João
family name: M. C. Teixeira
name: João M. C. Teixeira

joss.05983
type: ScholarlyArticle
name: DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning
pagination: 5983
url: https://doi.org/10.21105%2Fjoss.05983