The web server works via integrating molecular docking and interaction fingerprinting methods. It allows user to upload any small molecule of interest for predicting its kinase profile to all or selected kinase structures, and to visually inspect the predicted binding pose as well as the superimposition of the predicted pose with the crystal ligand. Our goal is to provide a useful, easy-to-use web server for kinase profiling. The help document is as below.
Query Structure - It allows user to submit a single molecule of interest via multiple ways, including the Mol2/SDF format, the SIMILES format, or drawing a chemical structure. It is recommended providing the single drug-like molecule or natural product with an optimal conformer stored in Mol2/SDF format. If the uploaded molecule does not have 3D structural information, the server will automatically convert it into a single 3D conformer.
Database Setup - By default, the entire kinase structural database is selected for kinase profiling for the query molecule. It also allows user to specifically select part of the database for kinase profiling. For example, the user can select a specific Kinase Group, e.g. ‘CMGC’, to profile the query molecule. Also, the user can select a set of kinases according to kinase family, ligand type, binding site, and disease, or any of the kinase structures for kinase profiling.
Job Detail - The user need to give a description of the job title, and a contact email for the reminder of the job status.
Submit - The user can submit the job when all the parameters are set up. Once the job is submitted, one job id will be generated, through which the user can check the job status and extract the results.
The user can check the job status by the generated job id. Note that it may take a few seconds for the check operation. Due to the limitation of the server load, the submitted jobs will be pushed into the queue before running.
Currently, the database contains 4,219 curated kinase-ligand complex structures, corresponding to 396 binding sites of 297 human kinases covering 106 kinase families. It also involves key residues, kinase downstream molecules, and associated diseases, providing additional information for kinase profiling. The database is searchable by PDB code, kinase name, kinase group, kinase family, downstream molecule, disease, ligand type, and binding site.
The user can download all of the curated kinase-ligand complex structures (pdb format), the separated kinase structures (pdb format) and ligand structures (mol2 format), and the kinase information (txt format) via the "DOWNLOAD" page.