kelly1210 / klifs_utils

Utility functions to work with KLIFS data

klifs_utils

This package has been moved to and extended in the opencadd package.

Please checkout the documention for the new package here.

Utility functions to work with KLIFS data

KLIFS

The klifs_utils package offers functions to interact with data from KLIFS (remotely and locally).

What is KLIFS and who created it?

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS), developed at the Division of Medicinal Chemistry - VU University Amsterdam, is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them

• KLIFS database: https://klifs.vu-compmedchem.nl
• KLIFS online service: https://klifs.vu-compmedchem.nl/swagger
• KLIFS citation
  • Description of the database itself (J. Med. Chem. (2014), 57, 2, 249-277)
  • Description of the online service (Nucleic Acids Res. (2016), 44, 6, D365–D371)

Installation

1. Download GitHub repo:

   git clone https://github.com/volkamerlab/klifs_utils.git

   The library lives now in this example path /path/to/klifs_utils.

2. Install and activate conda environment klifs_utils:

   cd /path/to/klifs_utils/devtools/conda_envs/
   conda env create -f env.yaml
   conda activate klifs_utils

3. Install library in conda environment while being in path /path/to:

   pip install klifs_utils

Alternative if you already have the klifs_utils environment installed:

pip install https://github.com/volkamerlab/klifs_utils/archive/master.tar.gz

Usage

Check out the klifs_utils tutorial (Jupyter notebook):

/klifs_utils/docs/tutorial.ipynb

Work with KLIFS data from KLIFS server (remotely)

The klifs_utils.remote module offers you to access KLIFS data from the KLIFS server.

This module uses the official KLIFS API: https://klifs.vu-compmedchem.nl/swagger.

Work with KLIFS data from disc (locally)

The klifs_utils.local module offers you to access KLIFS data from the KLIFS server. In order to make use of the module's functionality, you need a KLIFS download folder KLIFS_download with the following structure:

└── KLIFS_download
    ├── KLIFS_export.csv           # Metadata file
    ├── overview.csv               # Metadata file
    └── HUMAN     	               # Species name
        ├── AAK1                   # Kinase name
        │   ├── 4wsq_altA_chainA   # PDB ID, alternate model ID, chain ID
        │   │   ├── complex.mol2
        │   │   ├── ligand.mol2
        │   │   ├── protein.mol2
        │   │   ├── pocket.mol2
        │   │   └── water.mol2
        │   └── ...
        └── ...

Download KLIFS data from: https://klifs.vu-compmedchem.nl

Library structure

The libraries structure looks like this, trying have the same API for both modules local and remote (whenever possible):

├── local/
│   ├── coordinates/
│   │   ├── complex.py
│   │   ├── ligand.py
│   │   ├── protein.py
│   │   ├── pocket.py
│   │   └── water.py
│   ├── initialize.py
│   ├── interactions.py
│   ├── kinases.py
│   ├── ligands.py
│   └── structures.py
├── remote/
│   ├── coordinates/
│   │   ├── complex.py
│   │   ├── ligand.py
│   │   ├── protein.py
│   │   └── pocket.py
│   ├── interactions.py
│   ├── kinases.py
│   ├── ligands.py
│   └── structures.py
└── util.py

This structure mirrors the KLIFS Swagger API structure in the following way to access different kinds of information both remotely and locally:

• kinases (in KLIFS called information): Get information about kinases (groups, families, names)
• interactions: Get interaction fingerprint via structure_ID
• ligands: Get ligand information
• structures: Get structure information
• coordinates (in KLIFS part of structures): Get structural data (structure coordinates)

Note: In order to use the local module, it is necessary to initialize a metadata file (local.initialize module).

Copyright

Copyright (c) 2020, Volkamer Lab

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.