• Home

• Small Molecules: Hit identification

• Small Molecules: Hit-to-Lead optimization

• Small Molecules: physicochemical properties

• Small Molecules: ADME

• Small Molecules: Toxicity

• Small Molecules: Selectivity

• Antibodies: Humanization and Optimization

• Protein Modeling. Discovery

• Protein Modeling: HERG binding

• Protein Modeling: Albumin binding

• Quantum Discussions Forum    

You access the old version of our website. Please point your browser to our new home page.

Docking a small molecule

Description: Finds the position of a small molecule in the active site of a given protein with the minimum value of the free binding energy and predicts the IC50 of the ligand.

Requirements: The Ligand Docking Module requires 3D structures of a protein and a small molecule. The position of the active site of the protein should be known. Protein structures can be downloaded from the Protein Data Bank, as well as from some other sources of 3D biological macromolecular structure data. The protein and the small molecule structures should be uploaded with the .pdb format (or any standard formats like .hin, .mol2 etc.). The small molecule 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
• Accuracy of the prediction: Absolute deviation – 8 kJ and relative deviation – 15% (see Proof of consept_IC50).

Upload a protein and a small molecule.