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The IC50 of a Protein-Protein Complex

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

BACKGROUND: The IC50 calculation requires 3D structures of a protein-protein 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.

Note: This procedure does not provide docking one protein against another.

After selecting Tools->IC50 of a protein-ligand complex, the following procedures takes place:

Selecting Proteins

Make sure that both proteins are displayed.

Select one protein by clicking on it.

Select another protein.

Both proteins will be zoomed in and shown in sticks.

Press the Next button.

Selecting Essential Metal Ions and Hetatoms in the Active Site (if any)

BACKGROUND: The proteins can interact with metal ions and hetatoms in the active site. Correct energy calculation should involve all of the important structures within the active site.

After selcting proteins, all structures within the active site will be shown in the Names Panels.

You can remove any structure from the list.

Press the Next button.

Adding hydrogen atoms to the proteins and to the hetatoms

BACKGROUND: Most sources of 3D structures provide molecules only with heavy atoms, without hydrogen atoms. There is also no information on bond types (single, double and etc.) and protonation state (adding or extracting a hydrogen atom depending on the pH and the chemical group). But it is essential for Quantum's calculations to have the right number of hydrogen atoms in molecules. This procedure helps to do this.

You have three choices here:

· Go to the next step - "Calculate IC50"- if you think the proteins and all other structures in the active site have the right number of hydrogen atoms.

· Use the Build Model option from the Wizard to set the protonation state and add hydrogens by using Quantum's algorithms. We recommend this option.

· Use Builder to manually set bond types and add/remove hydrogen atoms.

Press the Calculate IC50 button.

Calculations and Results

All stages of the process are displayed on the Progress Bar and in the Information Panel.

When the calculation is finished you can see the results in a window that will appear instead of the Information Panel.

The window includes:

· 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

Note: Free binding energy is equal to the sum of all listed contributions (E es, E vdw, TdS and E tor). In our calculations, IC50 is 5.82 x (E bind).

You can compare the initial and final positions of the ligand by using Viewer. The procedure will create the object ligand_pos with final coordinates.

You can also save the report in HTML format, which is readable for most spreadsheet applications.

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