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IC50 of a protein-ligand complex

Description: Calculates the free binding energy and predicts the IC50 of any protein-ligand complex with known coordinates.

Requirements: The IC50 calculation requires 3D structures of a protein-ligand complex. In particular, such structures can be downloaded from the Protein Data Bank, as well as some other sources of 3D biological macromolecular structure data. The protein-ligand complex should be uploaded with the .pdb format (or any standard formats like .hin, .mol2, .sdf etc.). The ligand has to have not more then 25 flexible bonds.

Output/Results:

You will receive a .pdb file with coordinates of the docked ligand and the table with the information as follows:

  • Name - name of ligand
  • IC50 uMol/L - IC50 value
  • E bind, kJ/mol - free binding energy
  • E es, kJ/mol - electrostatic and solvation energy
  • E vdw, kJ/mol - short range electrostatic and exchange and Van der Waals energies
  • TdS, kJ/mol - entropy contribution
  • E tor, kJ/mol - ligand internal energy change
  • Charge, Mass, Flex.bonds - total charge, mass and number of flexible bonds of the ligand
  • RMSD, A - root mean square distance between the initial and final positions

Accuracy of the prediction: Absolute deviation – 8 kJ and relative deviation – 15% (see Proof of consept_IC50).

Upload all necessary information.

Your Name
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PDB identification
Ligand name
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