Editing Azahar (section)

=== Monte Carlo ===
This feature is still experimental

A Monte Carlo with Minimization (MCM) is a global optimization method that have proven very efficient to sample the conformational states of complex molecules like proteins, It was first published by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC299132/ Li and Scheraga], and is some circles is also know as basin hopping. Briefly, the conformational search is done by perturbing a torsional angle (psi, psi, omega or chi), follow by and energy minimization and the new (minimized) conformation is accepted or rejected following the Metropolis-criteria. If the conformation is accepted the next iteration start from the new conformation, otherwise the old conformation is perturbed again.

From the GUI the user can choose the number of iterations to run, whether or not to use a SASA model to take into account the solvent contribution, and whether or not to start from a random conformation.

After the  MCM procedure is completed the user will get:

* one .pdb file for each accepted conformation. 
* one multi-state .pdb file (automatically uploaded at the end of the run)
* one .pdb file for the conformation with the minimum energy.
* a plain text listing the energy of each saved conformation


The internal energy is computed using the MMFF94 force field (as implemented on open-babel) and the contribution of the solvent is approximated using a SASA model (the validity of the SASA model for glycans and the relative weight of the internal and salvation energies needs further test).