ProteinsPlus provides a wide-range of tools for structure-based drug discovery and structural bioinformatics. This repository provides examples on how use the proteins.plus API programmatically.
This project is developed at the Universitaet Hamburg, ZBH - Center for Bioinformatics by the group of Matthias Rarey.
Interactive examples can be found for:
- Protoss: Hydrogen prediction
- DoGSite: Binding site prediction
- PoseView: 2D images of protein-ligand interactions
- SIENA: Binding site similarity search
- EDIAscorer: Assessing electron density fit of individual atoms
- Molecule handler: Working with proteins and ligands
- StructureProfiler: Structure quality analysis
All notebooks can alternatively be run locally using jupyter notebook. We suggest using conda to manage the dependencies. You can generate a conda environment with all necessary dependencies using the following command:
conda create -n examples -c conda-forge -c anaconda python=3.7 nglview biopython jupyter requests rdkit
conda activate examplesSome notebook cells are colab specific. These may fail in jupyter notebook, but will not influence the rest of the notebook.