BetaCavityWeb
● Automatic and fast computation of molecular cavities and their geometric properties via
● Voronoi diagrams and beta-complexes

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  - BetaCavityWeb
  - Output format
  - System requirement
Manual & Examples
(PDB code: 5osa,
# atoms: 12,650,
# voids: 218, # channels: 26, passing solvent:1.4 Å
gate-defining solvent:7 Å,
Max. Depth(50%) + Vol. (50%))

BetaCavityWeb Automatic and fast computation of molecular cavities and their geometric properties via Voronoi diagrams and beta-complexes.    more...

1. Input molecule

    Please enter a PDB ID or click the "browse" button to upload a PDB file.
    - PDB ID:
    - Upload (PDB file):
    * For atomic radii, Bondi radius set is used (A. Bondi, 1964).

2. Cavity type

    2.1 Channels
    • Enter Passing Solvent Radius (Å)
      ( van der Waals cavity Lee-Richards (solvent accessible) cavity )
    • Enter Gate-definiing Solvent Radius (Å)
    2.2 Voids
    • Solvent Radius (Å)

3. Prioritization criteria

    - Molecular Depth: Maximum (%) Average (%)
    - Molecular Size   : Volume    (%) Area       (%)
    * Summation of all weights should be 100(%).

4. Submission

  * Citing BetaCavityWeb*
   J.-K. Kim, Y. Cho, M. Lee, R. Laskowski, S.-E. Ryu, K. Sugihara, D.-S. Kim, BetaCavityWeb: a webserver for    molecular voids and channels, Nucleic Acids Research, (doi: 10.1093/nar/gkv360), 2015.

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