· Delarue web servers
· Nomad Flow-chart
· Normal Mode calculation
  · Examples (Movies)
  · Submit a job (from PDB file)
  · Split trajectory (for MR)
  · Generate decoys (MixMod)
  · Elastic Energy (Perturb. Anal.)
· Overlap coefficients
  · Submit a job
  · Include Profit
· X-Ray refinement
  · Standard refinement
  · Screening Mol. Repl. Solns.
· EM refinement
  · Documents/Examples
  · Get Structure Factors
  · Submit a job (no NCS)
  · Submit job with NCS
· Docking refinement
  · Submit a job
· Force field methods
  · Energy minimization
  · Gromacs NMA
· References
· Homes/Links
· Job queue status

Docking refinement

This server refines one of the structures in docked pair, while the other one is assumed to be rigid. You must provide/choose:
  • The PDB file of the structure to refine (i.e. the flexible one).
  • The PDB file of the fixed structure in the pair, with coordinates so that it is placed in the (approximate/believed) docked position.
  • Number of normal modes to use, and parameters to determine them.
  • Optimization metod (scanning or minimization) to use.
  • Electrostatic weight relative to Lennard-Jones (normally 1.0).
  • Optional restraint coefficients on mode amplitudes.
The result of the optimization is a refined version of the flexible PDB structure.

Your email adress: (Recommended, for notification)



Job title: (Only alphanumerical characters)



PDB file of the flexible structure to refine (Ex: 1GGG_h.pdb):



PDB file of docked fixed structure (Ex: glucose.pdb):



The Lennard-Jones parameters of the structures will be assigned automatically from the CHARMM19 force field, but the charges should be written to the B-factor field in each file, since the automatic assignment algorithm often has problems with special residues or small ligands. For amino acid residues you can use the automatic method we provide here.


Number of normal modes to use (max 106):
Modes 1--6 are rigid-body, and should only be included if you are unsure about the relative positions of the structures.
First mode:   Last mode:


Parameters for normal mode analysis

For help on these parameters, see the detailed comments on the NMA calculation page.

Distance weight parameter (Ångström):



Cutoff to use for mode calculation (Ångström):



Normal mode calculation method to use (advanced):
       


Parameters for the refinement

Optimization method to use (advanced):




Electrostatic weighting relative to Lennard-Jones:



Mode restraint coefficient k:



Unrestrained amplitude range (if restraints are used):
Restraints are applied when amplitudes exceed this value.




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 files should be in PDB format, with only a single structure (no multiple models). Atoms marked with alternate residue flags will be removed. Whatever atoms are in the file will be used for the calculation. The length of each mode vector will be 3*natoms. Note that it is crucial to make at least a rough superposition of the docked structures before submission; this server only attempts refinement, not the molecular recognition part of docking.

  • Parameters for the normal mode analysis are described on this page.

  • For the optimization method it is slightly more stable to using the scanning approach rather than minimization, and it can also surmount potential energy barriers. However, if you use restraints on the mode amplitudes the minimization can also be useful. Since all mode amplitudes can vary in parallel for the minimization alternative, it is recommended to use fewer modes in that case.

  • An electrostatic weight of 1.0 corresponds to using the vacuum value of the dielectricity coefficient, while e.g. 0.25 means a relative dielectricity of 4.0.

  • Applying restraints makes the refinement much more stable, at the cost of some loss in the best possible cRMS decrease. The restraint potential is of the form 0.5*k*x^2, where x is the part of the amplitude that exceeds the unrestrained range. This approach is commonly used for NMR distance restraints: the amplitude can thus vary freely for small values, but if it gets too large we apply a restraining term. Both the range and coefficient can be specified.



  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:50 August 03, 2006.