· Delarue web servers
· PDB_Hydro Flow chart
· Modify PDB structures
  · Fix missing side chains
  · Flip HNQ side chains
  · Refine sidechain torsions
  · Single point mutations
  · Change sequence (decorate)
  · Generate missing loops
· Solvate PDB structures
  · Assign charges (PQR)
  · Run AquaSol
· References
· Homes/Links
· Job queue status

Solvate a PDB file

This web-server solves a Generalized Poisson-Boltzmann Equation, where the solvent is represented as an assembly of Langevin dipoles of finite size and variable density, orienting themselves in the electrostatic field of a (fixed) macromolecule (the solute), in the presence of free ions of given concentration.
All species are put on a grid to treat the size-exclusion problem. The equation is solved using the multi-grid method.
This is the work of Cyril Azuara for his Ph.D. thesis, using formalism developed in collaboration with Henri Orland (IPhT, CEA, Saclay, France) in 2005-2008.
This web site is fully described in the following publication (NAR Web server issue).

A full description of the method has been published shortly afterwards in Biophys. J (2008).

The program has actually been accelerated by a factor of 20 in AquaSol by Patrice Koehl (see Menu on the left).
If you are interested in getting the code, please contact either Koehl@cs.ucdavis.edu or marc.delarue@pasteur.fr.

Constructing polar hydrogen atoms and assigning partial charges can be done on line using the menu on the left.

Here is the kind of plot that can be obtained on a typical homodimer (TMP kinase):
-left: poorly solvated regions are in red (drawn with PyMol)
-right: water molecules have been placed (drawn with PyMol)

The dimerization interface is clearly seen as poorly solvated.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 12:05 May 09, 2016.