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Protein-ligand binding

This section outlines the calculation of the electrostatic binding energy for the protein kinase A complex with the inhibitor balanol. This example was provided by Chung Wong and is related to the work described in Wong CF, et al. J Med Chem, 44 (10) 1530-1539 (2001).

PQR files

The PQR files were prepared by Chung Wong from an energy-refined version of PDB file 1BX6 with CHARMM22 charges and radii. The individual PQR files can be dowloaded:

Important

You may have to right-click the links to save, rather than display, the PQR files.

These PQR files can be visualized via VMD: 


        $ vmd -pdb file.pqr
where file.pqr is the name of the downloaded PQR file. An example of the complex structure is shown in the following figure.

Figure 1. PKA-balanol complex

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Ion-ion desolvation Visualization of the electrostatic potentials