GalaxyWEB

A tool for covalent ligand docking that predicts binding poses of covalent ligands.

Help

• Method Information
• Input Files:
• PDB File: Protein structure (≤1000 AA). Format info
• Ligand File: Ligand structure in mol2 format (≤150 atoms)
• Covalent Geometry Options:
• Option 1 (Recommended): Ligand mol2 file includes two protein link atoms (covalently linked atom and its neighbor, e.g., SG,CB). Atom names must match the protein PDB file.
• Option 2: Use reference PDB structure to extract covalent geometry. Requires reference file and linked residue/atom info for both protein and ligand.
• Option 3: Unknown geometry. Protein atoms are added to the ligand link atom using typical bond geometry.
• Note: Ligand must be in post-reaction form in all cases.
• E-mail Notification: Providing an email enables automatic notifications. Otherwise, bookmark the report page.

Example

Option 1: Ligand-embedded protein atoms (Recommended)

• Fill Example Data
  Note: File uploads must be done manually.
• Receptor file: receptor.pdb
• Ligand file: ligand.mol2
• Target residue: 25A
• Binding Pocket Residues: 25A,65A,158A
• Protein Link Atoms: SG,CB
• Report: [View]

Option 2: Reference Geometry

• Fill Example Data
  Note: File uploads must be done manually.
• Receptor file: receptor2.pdb
• Ligand file: ligand2.mol2
• Reference PDB file: reference.pdb
• Target residue: 25A
• Binding Pocket Residues: 25A,65A,158A
• Reference protein residue & link atom: 25A,SG
• Reference ligand residue & link atom: 280A,CM
• Input ligand link atom: CM

Option 3: Unknown

• Fill Example Data
  Note: File uploads must be done manually.
• Receptor file: receptor3.pdb
• Ligand file: ligand3.mol2
• Target residue: 82B
• Binding Pocket Residues: 68B,82B
• Input ligand link atom: S16