SoftwareApplication
identifier: 10.5281/zenodo.3735041
name: DeepRank
description: Deep learning framework for data mining protein-protein interactions using CNN
description: - Predefined atom-level and residue-level PPI feature types, e.g. atomic density, vdw energy, residue contacts, PSSM, etc. - Predefined target types, e.g. binary class, CAPRI categories, DockQ, RMSD, FNAT, etc. - Flexible definition of both new features and targets - 3D grid feature mapping - Efficient data storage in HDF5 format - Support both classification and regression (based on PyTorch) DeepRank is a general, configurable deep learning framework for data mining protein-protein interactions (PPIs) using 3D convolutional neural networks (CNNs). DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models. #### Features: - Predefined atom-level and residue-level PPI feature types, e.g. atomic density, vdw energy, residue contacts, PSSM, etc. - Predefined target types, e.g. binary class, CAPRI categories, DockQ, RMSD, FNAT, etc. - Flexible definition of both new features and targets - 3D grid feature mapping - Efficient data storage in HDF5 format - Support both classification and regression (based on PyTorch)
code repository: https://github.com/DeepRank/deeprank
author: https://orcid.org/0000-0003-1791-7555
author: 0000-0002-2613-538X
author: https://orcid.org/0000-0001-7369-1322
author: https://orcid.org/0000-0002-0043-3055
author: https://orcid.org/0000-0002-7635-9533
author: https://orcid.org/0000-0002-8094-4532
author: https://orcid.org/0000-0002-1409-8358
author: https://orcid.org/0000-0001-9589-2694
keywords: Machine learning
keywords: Optimized data handling
keywords: Big data
programming language: C
programming language: Makefile
programming language: Python
programming language: R
programming language: Shell
license:
  creative work: creativeWork
    name: Apache-2.0
reference publication: s41467-021-27396-0

https://orcid.org/0000-0003-1791-7555
type: Person
given name: Francesco
family name: Ambrosetti
name: Francesco Ambrosetti
affiliation: Organization
  name: Utrecht University

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

https://orcid.org/0000-0001-7369-1322
type: Person
given name: Alexandre M.J.J.
family name: Bonvin
name: Alexandre M.J.J. Bonvin
affiliation: Organization
  name: Utrecht University

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

https://orcid.org/0000-0002-7635-9533
type: Person
given name: Lars
family name: Ridder
name: Lars Ridder
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0002-8094-4532
type: Person
given name: Sonja
family name: Georgievska
name: Sonja Georgievska
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/0000-0001-9589-2694
type: Person
given name: Nicolas
family name: Renaud
name: Nicolas Renaud
role name: eScience Research Engineer
affiliation: Organization
  name: Netherlands eScience Center

s41467-021-27396-0
type: ScholarlyArticle
name: DeepRank: a deep learning framework for data mining 3D protein-protein interfaces
url: https://doi.org/10.1038%2Fs41467-021-27396-0