KinaseDocker² Database

Database

The .sqlite file in this dataset is released as part of the KinaseDocker² research. It serves as a ML-ready dataset of small molecule docked poses in a curated set of kinases. Please refer to the publication for more information. 

The .knwf file provides an easy to use graphical interface to query the dataset released. Follow the instructions below to get started.

KNIME GUI Installation

KNIME can be downloaded free of charge from KNIME.com. When installed, the workflow downloaded from this repository can be imported through Local Space ->Import workflow. The software will warn that there are missing dependencies (KNIME Base Chemistry nodes, KNIME-CDK, KNIME Python Integration) and propose to search and install these. Approve, and after a restart of KNIME the workflow should load.

Usage

To use, the location of the downloaded .sqlite file needs to be configured by double clicking the gray node in the green box. Browse to the .sqlite file and click OK. Execute the node by clicking the Execute button in the top bar.

Now, either use the red-boxed part of the workflow to browse based on a kinase of choice or use the blue-boxed portion of the workflow to query based on compounds. The instructions per node are in the workflow, but typically it requires execution of the node (shortcut: F7 or click Execute in the top bar) and opening the View it generates (shortcut: F10 or hover over node and click magnifying glass). Some nodes require configuration: either the choice of docking engine (Vina / DiffDock) or the folder to write files into.