ProfKin Help Document

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.

    1. (a) Submit Job
      Job Submit Panel
      Click on the figure to get more details

      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.

      A file should contain exactly one molecule.
      The maximum size of the uploaded file is 10 MiB.

      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.

      Advanced Options - The user can set up the IFPscore and Cvalue cutoff. The IFPscore denote the similarity between the docking pose interaction fingerprints (IFP) and the reference IFP models for each kinase, whereas the Cvalue is calculated as a comprehensive index for the final kinase ranking. By default, the IFPscore and Cvalue cutoff are set as 0.5 and 10.0, respectively.

      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.

    2. (b) Check Job
      Status Check Panel
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      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.

      For now, we allow up to 2 running jobs per user.
      The results for the jobs will be remained on the server for no shorter than 45 days.
    3. (c) Get Results
      Result Display Page
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      The user can get results using the generated job id. The kinase profile is ranked by Cvalue. For each kinase, the predicted pose of the query molecule can be viewed together with the crystal ligand to visually inspect their resemblance.
    Database Search Page
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    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.

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Updated: 2021-05-20 | Local time: 2024-05-23 | Contact us
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