Welcome to the EEF1 Server!



EEF1 (Effective Energy Function 1 [1]) is a combination of a modified form of the charmm 19 force field [2] and an implicit solvation model. EEF1 has given encouraging results in the discrimination of native conformations from misfolded decoys [3]. It could, therefore, be useful in protein structure prediction [4].

This server will take your PDB-format coordinates, perform 300 steps of energy minimization using EEF1 and the Adopted Basis Newton Raphson method, and email you the final energy and its decomposition. Obviously, the energy of a single model is meaningless. Only a comparison of the energy of a number of models is helpful for selecting the best one.

The resulting minimized coordinate file will be in CHARMM format. This format is recognized by rasmol, vmd and other programs and can be converted to PDB using Babel. If you don't have Babel you can use the following fortran program: charmmtopdb.f.

Please provide the following information.

Name:
E-mail:
ONE address only and in CORRECT FORMAT please.
Organization:
File to upload:
Your file should be in PDB format.

A modest contribution from the
Lazaridis lab
Chemistry Department
City College of CUNY
New York City

References

1. Lazaridis, T., Karplus, M. "Effective energy function for proteins in solution", Proteins , 35:133-152 (1999)

2. Neria, E., Fischer, S., Karplus, M. "Simulation of activation energies in molecular systems", J. Chem. Phys. , 105:1902-21 (1996)

3. Lazaridis, T., Karplus, M. "Discrimination of the native from misfolded protein models with an energy function including implicit solvation", J. Mol. Biol., 288:477-487 (1999)

4. Lazaridis, T., Karplus, M. "Effective energy functions for protein structure prediction", Curr. Opin. Struct. Biol., 2000, in press.

This server has been developed by Guoliang Qian. Comments and report of problems (tlazaridis at ccny.cuny.edu) will be greatly appreciated.

Last modified 10 April 2004