PROTEIN STRUCTURE OPTIMIZER

The protein structure optimizer minimizes the energy of the protein structure using a combination of steepest descent and conjugate gradient minimization algorithms. The software uses Cornell et al, 1995 Force Field equation.

    Instructions :

  1. Select a PDB file using the browse button. ( the file should strictly conform to the PDB format )

  2. Choose the desired algorithm and the respective step size. ( to neglect any of the two algorithms specify zero as the step size against it )

  3. Specify the dielectric constant.

  4. Click the submit button to get the results and the minimized structure.

    Please note :

  • The PDB file should not have any missing residues.

  • The terminal atoms should be present.


Protein Structure Optimizer
 Method 1 :      Step size :
 Method 2 :      Step size :
 Dielectric :
Input PDB file :
Upload the file in the given format [Sample File]

Number of Hits since 20th April 2008: 7806

REFERENCES
  1. "Tunneling through the energy barriers towards the native structure of protein", Mishra A., Mittal A., Jayaram B.(Manuscript in prepration).