Step 1: Input molecule and conditions

Prepare a SMILES string or chemical structure for the compound of interest. When you enter the 'Prediction' page, you can process the prediction step.

CRITICAL STEP: There are 2 ways to choose for input molecule:

Choose 1: Enter SMILES directly

• Enter or paste a valid SMILES string into the input box at the top
• Supports both canonical and noncanonical SMILES formats
• Ensure the SMILES string is properly formatted without any errors

Choose 2: Draw the molecule

• Use the built-in molecular drawing tool to construct your molecule
• Click the "Get SMILES" button after drawing to convert your structure to SMILES format
• The converted SMILES will automatically appear in the input box

Additional fatures:

• Example Molecule: If you want to test the system, you can use the provided example (Aspirin/Acetylsalicylic acid) by clicking the "Use this example" button
• Submit: After entering or drawing your molecule, click the "SUBMIT" button to start the prediction process
• Page Navigation: The page will automatically jump to show the calculation progress
• Resource Monitor: Hover over the resource icon in the top right corner to view resource usage and queue status

Important notes:

• Remove any salts or solvent molecules from your structure before submission
• Verify that your SMILES representation is valid and error-free
• Do not navigate away from the page while the calculation is running
• The waiting time is typically within one minute for standard predictions
• You can monitor the calculation progress and resource availability through the status indicators

Step 2: Result view and modification options

Once the calculation is complete, the results page will display comprehensive information about your molecule in three main sections:

1. Input molecule properties:

• Input SMILES string and 2D molecular structure visualization
• Detailed molecular properties including:
  • Physicochemical parameters (cLogP, MW, TPSA, etc.)
  • Structural features (nHet, nRing, HBD, HBA)
  • Predicted properties (Toxicity status, Bioavailability percentage)
• Color-coded metabolic probability indicators

2. Metabolism of input molecule:

• Tabulated results showing predicted metabolites with:
  • Rank ordering of metabolites
  • 2D structures of metabolites
  • SMILES representations
  • Reaction templates (with "More info" button for detailed reaction information)
  • Reaction types
  • Toxicity predictions
  • "Modification" options for each metabolic site

3. Modification Options:

• Quick modification:
  • Available through the "Modification" button in the metabolite table
  • Targets specific metabolic sites you are interested in
  • Processing time: 1-2 minutes
• Precise modification:
  • Accessible via the "Click for modifying all metabolic sites using 3D shape similarity" button
  • Comprehensive optimization of all metabolic sites
  • Processing time: approximately 1 hour
  • Results delivered via email (optional)
  • Generates a unique results URL for accessing the modifications

Additional features:

• Detailed reaction information available through "More info" buttons
• Reference links to source databases where available
• Progress indicators for both quick and precise modification processes

Step 3: Modification results and analysis

After selecting and running the modification process, the system will display comprehensive optimization results in an interactive interface:

Fragment-based molecular recommendation process:

• Identification of fragments associated with the molecule's metabolic sites
• Fragment replacement and linkage optimization
• Conformational screening and validation
• Ranking using multi-criteria evaluation functions

Results display features:

• Interactive results table:
  • 2D molecular structures of optimized compounds
  • SMILES strings for each recommended molecule
  • Comprehensive scoring metrics (LogP, QED, SA, F, Toxicity)
  • Overall optimization score and 2D similarity to parent molecule
  • "Optimize" button for iterative refinement
• 3D molecular visualization:
  • Interactive 3D alignment viewer showing query and candidate molecules
  • Real-time comparison of original and modified structures
  • 3D shape similarity assessment