- 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
- For more details, please refer to the
[download pdf] (PNAS, 2005) paper.
conformations are built by initially assigning each residue to one of
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
insufficient to consider the simultaneous influence of both the
sequence and conformation. Hence, we adopt a strategy based upon pairs
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
of finding two consecutive residues ai
and ai+1 in basins bi
and bi+1 gives the Nearest
Neighbor correlation energy
,ai+1,bi+1) in terms of probabilities
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
effects. An individual residue contributes U(ai,bi),
and an additional term dU(ai,bi
from each of the neighbors combines to give the total statistical
a polypeptide with N residues,
An equilibrium ensemble of
peptide chains is generated
from Monte Carlo (MC) simulations with this energy function. The
transitions consist in choosing a Ramachandran basin for randomly
residues and then accepting or rejecting the transition according to
standard MC criteria. Once the basins are assigned, the specific f,y
backbone angles within the basin are selected from occurrences in the
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.