Welcome to NanoShaper Web
Let's explore how to analyze molecular structures
Load Your Structure
You can load your structure in two ways:
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Upload PDB or PDBx/mmCIF File
Select and upload a structure file directly from your computer
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Enter PDB ID
Use a 4-character PDB identifier to fetch from the database
Configure Parameters
Adjust the following parameters:
Pocket Detection Parameters
Small Probe Radius: Default 1.6 Å (use 1.4 Å when hydrogens are present)
Big Probe Radius: Default 3.0 Å (increase to detect shallow pockets)
Surface Calculation Parameters
SES (Probe radius) and Skin (Smoothness) settings
Chain selection for analysis
Submit Your Job
After configuring parameters:
Add your email for job notifications (optional)
Click "Submit Job" to start the analysis
Monitor progress in Jobs Management
Viewer Controls
Explore your structure with:
Visualization
- 3D controls
- Surface views
Features
- Screenshots
- Fullscreen
Pockets Table
Access detailed information:
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View pocket details
Size, type, and other properties
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Interactive controls
Add/remove pockets from viewer
Resume Your Work
Continue your analysis anytime:
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Save your Session ID
Copy and store it securely
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Restore your session
All results and settings are preserved
Your data will be kept for 7 days
