· 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
· Job queue status
Solvate a PDB file
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).
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.
Page last modified 12:05 May 09, 2016.