· 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
· Include Profit step
· Without Profit!
· X-Ray refinement
· Standard refinement
· Screening Mol. Repl. Solns.
· EM refinement
· Get Structure Factors
· Submit a job (no NCS)
· Submit job with NCS
· Docking refinement
· Submit a job (refinement)
· Submit a job (scanning)
· Force field methods
· Energy minimization
· Gromacs NMA
· Job queue status
This server refines one of the structures in docked pair, while the
other one is assumed to be rigid.
You must provide/choose:
The result of the optimization is a refined version of the flexible PDB structure.
- The PDB file of structure to refine (i.e. flexible one).
- The PDB file of fixed structure in the pair, in the
(approximate/believed) docked position.
- Number of normal modes to use, and parameters to determine them.
- Electrostatic weight relative to Lennard-Jones (1.0).
- Optional restraint coefficients on mode amplitudes.
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
- 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
- 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
- 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.