RobustCavities Job Form

The fields are already populated with good default values for input parameters. However, you can modify these values a bit if you want. Hovering over the fields provides brief information about the input parameters.

  • PDB id of protein structure available on RCSB database.

  • Upload PDB file in text format.


  • Stability parameter quantifies perturbation allowed in atomic radii to make cavities stable. Suggested range is 0.00-2.00.

  • Persistence of cavity captures its importance, and is used to prune out unimportant cavities. Suggested range is 0.00-2.00.

  • Radius of the solvent. By default 1.40Å is taken as solvent radius which corresponds to radius of a water molecule.

  • Maximum possible perturbation in atomic radii for the current values of ε and solvent radius. Use higher values to connect many cavties via channels. Use lower values to preserve small cavities. Suggested range is 0.0-0.5Å.


  • Output file generation:

  •      (Unckeck for fast computation.)

  • Send the result link to this Email ID when the job is finished.


Contact

Suggestions, comments and feedback: Send email to tbmasood@csa.iisc.ernet.in