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
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)
-
Download GitHub repo:
git clone https://github.com/volkamerlab/klifs_utils.git
The library lives now in this example path
/path/to/klifs_utils
. -
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
-
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
Check out the klifs_utils
tutorial (Jupyter notebook):
/klifs_utils/docs/tutorial.ipynb
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.
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
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 calledinformation
): Get information about kinases (groups, families, names)interactions
: Get interaction fingerprint via structure_IDligands
: Get ligand informationstructures
: Get structure informationcoordinates
(in KLIFS part ofstructures
): 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 (c) 2020, Volkamer Lab
Project based on the Computational Molecular Science Python Cookiecutter version 1.1.