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DeepRank

Deep learning framework for data mining protein-protein interactions using CNN

60
mentions
8
contributors

Cite this software

What DeepRank can do for you

  • 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)
Logo of DeepRank
Keywords
Programming languages
  • Python 99%
  • R 1%
License
  • Apache-2.0
</>Source code

Participating organisations

Life Sciences
Life Sciences
Netherlands eScience Center
Radboud University Medical Center
Utrecht University

Reference papers

Mentions

Contributors

Contact person

Nicolas Renaud

Nicolas Renaud

Netherlands eScience Center
AB
Alexandre M.J.J. Bonvin
Utrecht University
Cunliang Geng
Cunliang Geng
Netherlands eScience Center
DM
Dario Marzella
Radboud University Medical Center
FA
Francesco Ambrosetti
Utrecht University
Lars Ridder
Lars Ridder
Netherlands eScience Center
LX
Li Xue
Radboud University Medical Center
Nicolas Renaud
Nicolas Renaud
Netherlands eScience Center
Sonja Georgievska
Sonja Georgievska
Netherlands eScience Center

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