SCORING FUNCTION FOR PROTEIN STRUCTURE EVALUATION


CRO Repressor Protein

This utility calculates energy of a given protein using an all atom energy based empirical scoring function.
The scoring function considers the non-bonded energy of a protein, expressed as a sum of three terms - electrostatics, van der Waals and hydrophobicity.
ETotal = ∑( Eel + Evdw + Ehpb )
Eel is the electrostatic contribution to the energy, Evdw is the van der Waals term, Ehpb is the hydrophobic contribution and the summation runs over all the atoms of the protein [1-4].

SCORING FUNCTION
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).
Validation of Scoring Function

The empirical scoring function is validated on 69 proteins and their 61974 decoys, belonging to twelve different publicly available as well as our own build decoy sets. Only those proteins are selected for which native structure is obtained via X-ray crystallography and are free from metal ions and prosthetic groups. Proteins which are fragments or mutlimers, or having mismatches in the number of atoms between native and decoys are also skipped. After addition of hydrogen atoms and subsequent minimization, energy calculations are carried out using the scoring function [4]. The minimized all atom decoys are given below.
S.No. Decoy sets References Number of Sequences studied Number of decoy structures investigated
(1) EMBL Holm & Sander, J Mol Biol, 225, 93-105 (1992). http://prostar.carb.nist.gov 7 10
(2) CASP1 Collection of structures for given targets in CASP1. http://predictioncenter.llnl.gov/download_area/ 2 12
(3) 4state_reduced Park & Levitt, J Mol Biol, 258, 367-392 (1996). http://dd.stanford.edu/ 5 3326
(4) Lattice_fit Samudrala & Moult, J Mol Biol, 275, 893-913 (1998). http://dd.stanford.edu/ 4 8000
(5) Lmds Kesar & Levitt, J Mol Biol, 329, 159-174 (2003). http://dd.stanford.edu/ 6 2634
(6) Fisa Simons et al., J Mol Biol, 268, 209-225 (1997). http://dd.stanford.edu/ 2 1000
(7) Fisa_CASP3 Simons et al., J Mol Biol, 268, 209-225 (1997). http://dd.stanford.edu/ 3 3098
(8) Hg_structal Samudrala et al., unpublished work. http://dd.stanford.edu/ 2 58
(9) Semfold Samudrala & Levitt, BMC Struct Biol, 2, 3-10 (2002). http://dd.stanford.edu/ 2 22667
(10) Rosetta Simons et al., Proteins : Struct Funct Genet Suppl 3, 171-176 (1999).
http://depts.washington.edu/bakerpg		 21 20484
(11) CASP5 Collection of structures for given targets in CASP5. http://moult.carb.nist.gov/ 7 614
(12) Homology http://scfbio-iitd.res.in/decoys/Homology/ 8 71
  Total   69 61974

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, (2005). (manuscript accepted)
SUGGESTIONS AND COMMENTS

Please feel free to send your suggestions and comments at scfbio@scfbio-iitd.res.in