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· 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 loops
· Solvate PDB structures
· Assign charges (PQR)
· Solvate using GPBL
· Place Waters
· All in one
· NEW !!! AQUASOL !!!
· Run AquaSol
· Job queue status
Flip last chi angle in Asn, Gln and His side chains by MFT
Crystallographers cannot really decide between an Oxygen or Nitrogen or Carbon atom type in an experimental
electron density map (unless this is a really high resolution map where one could see Hydrogens, i.e. better than 1 Angstrom).
Therefore the amide groups of Asparagine and Glutamine (N,Q) side chains are ambigous, up to a 180 degrees flip
of the last chi angle of their side chains.
The same is true for the aromatic cycle of Histidine (H).
In vacuo electrostatics can be used in a first approximation to decide which is the best local hydrogen bond network.
The resulting combinatorics (2**n possibilities, where n is the number of HNQ side chains, of the order of 20-50)
is too large to be searched exhaustively.
In the past Monte Carlo methods have been used to find the global minimum of the energy function (Nielsen and Vriend, Proteins, 2001, 43:403-12; Nielsen et al., Protein Eng., 1999, 12:657-62).
Here we present a simple implementation of Mean_Field_Optimisation techniques to solve this problem in a very
computationnaly efficient way (see Koehl and Delarue, 1994, J. Mol. Biol. 239:249-75)...
Input data formats
- The job title is just for your own identification, but note that
it will show up in the public job queue (but your results will not be public).
- The coordinate file should be in PDB format, with only a single
structure (no multiple models). Atoms marked with alternate residue
flags will be removed. Polar hydrogens will be generated internally.
Atoms with a HETATM card will be copied to the output file.