User Guide
How to create a computation job for Human Pathogenic Microorganisms Chemogenomics Knowledgebase (HPM-CKB)?
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To issue a new computation job, you first need to click on the BlueStart Analysis button from the Home page.
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Name your job and draw your molecule with the Molecular Editor. You can also paste in any pre-existing molecule structure in SMILES format via the Paste SMILES. In this way, please be aware that the pasted code should NOT contain any leading or trailing spaces. Hit Confirm to continue.
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Verify the graphic depiction of your molecule presented at the Molecular Editor canvas area. You can use the editor to modify it as needed and then select the specific species of pathogenic microorganisms via Target Species. Finally, you hit the yellow Create Job button below when it is ready to go. Your job will be created immediately and enqueued to be processed.
How to inspect prediction results?
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Once your job is created and enqueued, you will be brought to the home page of the newly created job where you are presented useful functionalities like Molecular Fingerprint, Molecular Model Download and BBB Prediction for the input molecule. Scroll down the page to access all the tools. Links to Results and Radar Chart can be found from the context-aware navigation bar where you will find prediction results of your job.
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The Results page can display results of your job in either table mode or cards mode for your conveniences. Toggle between views with the top right switch. In table mode you are provided multiple options to customize the view such as defining the pagination length and the sorting column. Results that are finalized will be presented with links to see detailed information about the protein, to download models or to compare between best matched known molecule. Also note that the sorting headers support multi-sorting by clicking multiple column headers one after another while holding SHIFT key at the same time.
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Switch to Radar Chart and you will see prediction result in graphics. A bunch of customization tools are provided. You can define molecule/target circle colors and sizes, text colors and sizes, border sizes and colors. You can also toggle visibility of interaction labels, display of molecular depiction. All nodes on the graph are also manipulatable. You can define position of every single nodes and by holding SHIFT or CTRL key you can even move the entire graph and multi-select nodes. Additional functionalities including exporting the plot to an image are coming soon. At the moment with Chrome you can Save image as by right clicking on the image.
How to use the customized large language model?
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To use the customized large language model (LLM)-PharmNavig, you first need to click on the Violet Bio-AI Assistant button from the Home page. Then you may start asking questions and get answers.
How to query protein information of pathogenic microorganisms?
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To search for protein information of pathogenic pathogens, you first need to click on the Proteins button in the menu bar, and then You can obtain relevant information.
