· 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)
  · Solvate using GPBL
  · Place Waters
  · All in one
  · Run AquaSol
· References
· Homes/Links
· Job queue status

Construct missing side chains from PDB file

It often happens that protein structure coordinates files (PDB) lack some atoms in some sidechains, simply because the electron density was not there to trace them, so that the crystallographers decided not to include them, even though the residue type is correctly assigned.

In some application(s) (rmsd calc., docking exp., electrostatic calc...) it is necessary to build the missing sidechain atoms.

Here we scan all possible rotamers for those residues whose sidechain atoms are missing from the original PDB file and choose the one with the lowest VdW energy. This is done sequentially and one residue at a time, while the rest of the molecule is kept "frozen".

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters - no space)

PDB file to be checked Ex: Example

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 conformation flags will be removed. Heteroatoms (HETATM) will be copied to the output file.

  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:10 May 12, 2017.