DeepRank

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

83
mentions
8
contributors
Get started
archived repository975 commitsLast commit ≈ 12 months ago147 stars26 forks

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
</>Source code

Participating organisations

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

Reference papers

Mentions

Contributors

AB
Alexandre M.J.J. Bonvin
DM
Dario Marzella
FA
Francesco Ambrosetti
Lars Ridder
Lars Ridder
LX
Li Xue
Sonja Georgievska
Sonja Georgievska
Nicolas Renaud
eScience Research Engineer
Netherlands eScience Center

Related projects

3D-Vac

Personalized cancer vaccine design through 3D modelling boosted geometric learning

Updated 8 months ago
In progress

DeepRank

Scoring 3D protein-protein interaction models using deep learning

Updated 20 months ago
Finished

Related software

DeepRank GNN

DE

DeepRank-GNN is the graph neural network of our DeepRank package. DeepRank GNN allows to train graph neural networks to classify protein-protein interface

Updated 3 weeks ago
87 2

pdb2sql

PD

Fast and versatile Python package that leverages SQL queries to parse, manipulate and process biomolecular structure files. The structure files should be in the PDB format and are available on www.rcsb.org.

Updated 29 months ago
8 2

PSSMGen

PS

Generates consistent PSSM and PDB files for protein-protein complexes

Updated 29 months ago
6 2