Sections


1.  Enter the file of protein sequence (FASTA format) :

   

2.  Enter the PDB library from which the statistical potential will be derived:

Library  

3.  Use Nearest Neighbor effects:             

NN:  

4. Number of conformations in ensemble:

#:

 (fewer means faster)

5. Enter your email address to which the result of the computation should be sent:

Email address:




Note: Computation times vary greatly depending on the server load.

Getting Started

  • To start a simulation, enter the required values in the fields on the left and click Submit. When the simulation is finished, the resulting ensemble will be sent to you via email.
  • For a quick overview, a short description of methods is provided below.
  • For more details, please refer to the [download pdf] (PNAS, 2005) paper.

Methods

  • Unfolded conformations are built by initially assigning each residue to one of five Ramachandran basins based upon their frequencies in the coil library.
  • A residue’s basin frequencies depend on its identity and that of the neighboring residues. However, the size of the coil library is insufficient to consider the simultaneous influence of both the neighbors’ sequence and conformation. Hence, we adopt a strategy based upon pairs (dimers) of residues. The monomer basin frequencies, P(ai,bi), are converted into energy units by

                U(ai,bi)= -RT ln P(ai,bi)        

    where ai is the identity of the ith amino acid that resides in the bi Ramachandran basin. Similarly, the joint probability, called the dimer library, of finding two consecutive residues ai and ai+1 in basins bi and bi+1 gives the Nearest Neighbor correlation energy term dU(ai,bi ,ai+1,bi+1) in terms of probabilities derived from the coil library,
  • .                              

    The local interactions that dominate the structure of the polypeptide chain can now be modeled by an energy function that includes first neighbor effects. An individual residue contributes U(ai,bi), and an additional term dU(ai,bi ,ai+1,bi+1) from each of the neighbors combines to give the total statistical potential for a polypeptide with N residues,


    .                           (4)

    An equilibrium ensemble of peptide chains is generated from Monte Carlo (MC) simulations with this energy function. The elementary transitions consist in choosing a Ramachandran basin for randomly determined residues and then accepting or rejecting the transition according to the standard MC criteria. Once the basins are assigned, the specific f,y backbone angles within the basin are selected from occurrences in the coil library for each residue type, independent of NN effects.
  •  To remove steric overlap, the dihedral angles are "nudged" withing the basin of each amino acid by  minimizing a simple excluded volume energy function for intra-basin relaxation.