SCORING FUNCTION FOR PROTEIN STRUCTURE EVALUATION
ProSEE (Protein Structure Energy Evaluation)


RMSD
Upload the file in the given format [Sample File]

             Input PDB file :

Instructions for using the Tool

  1. The input file is a minimized all atom protein in PDB format. The file should follow the format described in README; otherwise erroneous values will be generated. Currently the program works only for monomeric globular proteins.
  2. The program displays the electrostatics, van der Waals and hydrophobic components as well as total energy of the protein (kcal/mol).

REFERENCES
  1. N. Arora and B. Jayaram, J. Phys. Chem. 102, 6139-6144 (1998).
  2. N. Arora and B. Jayaram, J. Comp. Chem. 18, 1245-1252 (1997).
  3. M. A. Young, B. Jayaram and D. L. Beveridge, J Phys. Chem. 102, 7666-7669 (1998).
  4. Narang, P., Bhushan, K., Bose, S., and Jayaram, B. Protein structure evaluation using an all-atom energy based empirical scoring function. J. Biomol.Str.Dyn, 23, 385-406. (2006).
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