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  · Fix missing side chains
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  · Generate missing loops
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  · Solvate using GPBL
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Do single point mutations

Suppose we want to do a single mutation in a PDB file.
Here we first scan all possible rotamers for the residue to be mutated, with the rest of the molecule kept frozen.

Then the whole energy is minimized, thanks to a program due to Patrice Koehl (FixPDB in Toolkit_08).

The program will detect if the PDB file contains several chains; if so, it will do the same mutation simultaneously in all the chains. This is intended for symmetrical assemblies. If you need to do a mutation in only one subunit, send me an e-mail, I will try to set up this option in the near future.

Your email adress: (Recommended, for notification)

Job title: (Only alphanumerical characters - no space)

PDB file to be checked Ex: Example

Position to be mutated

Number of minimisation cycles

New amino acid type at this position :

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.

  • The position to be mutated assumes that the first position of the original PDB file is 1. Consequently, if it starts at, say, 5 and you want to mutate position 125 you should type 121 (n_wished - n_start + 1) in the box.

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