🧬 Custom Peptide Docking

Select an HLA-DQ protein and upload your peptide PDB file for direct molecular docking analysis.

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🎯 Perform Direct PDB Docking

Choose the receptor protein for docking analysis.
Supported format:
  • .pdb: Protein Data Bank format with 3D coordinates
Requirements:
  • Valid PDB format with ATOM records
  • 3D coordinates for all atoms
  • Peptide length: 3-50 residues
  • Max file size: 16MB
⏱️ Direct docking: 1-5 minutes | Simulation: 5-15 seconds
📋 How Direct PDB Docking Works
  1. Protein Selection: Choose your target HLA-DQ protein
  2. PDB Upload: Upload pre-modeled peptide PDB structure
  3. Structure Validation: Verify PDB format and coordinates
  4. Direct Docking: Perform molecular docking with AutoDock Vina
  5. Results: View 3D structures and binding scores
💡 Tips for Best Results
  • Use high-quality PDB structures with good geometry
  • Ensure your PDB contains only the peptide of interest
  • Remove any water molecules or other ligands
  • Verify that all atoms have 3D coordinates
  • Use peptides between 5-30 amino acids for optimal performance
  • Recommended: Generate PDB using PepFold4 for best accuracy