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· 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
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· Job queue status

Change the entire sequence (and side chains) of a PDB file

The new sequence is specified through an alignment file between the old and new ones. Its format should be MSF (example) as produced by PILEUP by GCG.

  • The first sequence MUST be exactly the template sequence (from PDB file).
  • The second sequence is the one to be modelled. This order is COMPULSORY.

    There is no loop building facility in this program, therefore there should be no insertion and no deletion (no gap) in the alignment (MSF) file.

    All side chain atoms are reconfigured using the Mean-Field algorithm (Koehl and Delarue, 1994, JMB, 239:249-75) and rotamers. See PDF here.


  • This can also be used to build models of the structure of mutants, or do protein design.

    N.B. The progam now has two options: it can either reconfigurate all sidechains or copy the side chains of those positions that are strictly conserved and reconfigurate only the non-conserved positions.

    See also Patrice Koehl web site.

    Your email adress: (Recommended, for notification)


    Job title (Only alphanumerical characters)


    PDB input file Ex: 1lzr.pdb


    Alignment file (MSF style!) Ex: 1lzr.msf


    Number of cycles (typically 25)


    Updating factor between cycles (typically 0.5)


    Method to use :
             

    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.

    • The alignment file specifies what will be the new sequence. The template sequence MUST be the first one, while the sequence to be modelled MUST be the second one! Here is an example: lyso.msf.

    • The Number of cycles specifies the number of refinement cycles.

    • The lambda factor specifies the speed of the convergence.




      Marc Delarue http://lorentz.dynstr.pasteur.fr
    Page last modified 18:40 August 07, 2006.