RobustCavities

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:
PDB id of protein structure available on RCSB database.
Or, Upload PDB file:
Upload PDB file in text format.
Consider HETATM records in the PDB file (excluding HOH)

*Epsilon:
Stability parameter quantifies perturbation allowed in atomic radii to make cavities stable. Suggested range is 0.00-2.00.
*Pi:
Persistence of cavity captures its importance, and is used to prune out unimportant cavities. Suggested range is 0.00-2.00.
*Solvent Radius (Å):
Radius of the solvent. By default 1.40Å is taken as solvent radius which corresponds to radius of a water molecule.
Maximum Perturbation (Å):
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:

Generate Skin Mesh representation of cavities.
(Unckeck for fast computation.)

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