Calculate Binding Energy

Upload Files, Adjust Parameters and Submit Job

Before submitting a job, prepare three PQR files for the biomolecule complex and its two components (component A and component B). This can be done by first downloading PDB files of the biomolecules from the RCSB Protein Data Bank, and then converting them to PQR files by using PDB2PQR. After preparing the PQR files:

  1. Upload the PQR files for the complex, component A, and component B separately.
  2. Adjust basic parameters, or use default parameter values.
  3. (Optional) Adjust additional parameters (located in tabs).
  4. Submit the job by clicking the "Run SDPBS" button.

Solver  ? Select a PBE solver.

Mesh Parameters for Protein Complex

Mesh Parameters for Protein Component A

Mesh Parameters for Protein Component B

This job may take a few minutes. When the job is complete, a free energy value, download link, visualization, and output log will be updated on this page.
Reload the page to run a new job.

View Results

After submitting the job, please wait patiently for your results.

When your results are successfully retrieved from the server, you should see the following changes on the page:

  • The "Electrostatic Binding Free Energy" section below should show a table summarizing the computation results.

Electrostatic Binding Free Energy

Submit a job to view the free energy values.