Voronoia contains a database of over 160.000 precalculated structures, including most of the structures found in the Protein Data Bank. You can browse these structures in a table on the subpage database.
To search a specific entry, click on the input field and type in the PDB-ID of the structure you wish to view.
You will be taken to the results subpage, where you can view and explore the data generated by Voronoia.
If you want to test out the submission process on Voronoia with an example, you can visit the submit page and click on the green icon in the lower left, under the grey box. This will take you to an already filled out form which you usually need to fill out yourself to submit a structure for calculation with Voronoia. You can play around with the input if you like or you can directly click on the green Analyse button. You need to wait a few minutes for the calculation to finish and after that you will be redirected to the results page, where you can analyse the example PDB with Voronoia.
Since not all known macromolecular structures are deposited in the database and you may wish to analyse unpublished structures, you can submit a new structure for calculation under the submit subpage.
To submit your structure you first need to upload a pdb file. You can click on the green button titled 'Upload a PDB' to browse your filesystem for a file to be uploaded, or you can drag and drop a file into the grey box with the dashed outline.
When you have uploaded a file, you will see a new form for submission appear. You need to enter an id, a unique string which identifies your job unambiguously. Alternativly you can also click on the dice icon, which will generate a random tag for you. If you want to be notified when your results are ready, you can optionally enter an email adress.
Once you have entered all required informations, you can click on the green submit button on the bottom of the page. You will now be redirected to the progress site, where you can view the status of your job while it is in queue or being calculated.
The calculation may take a while (up to 15 minutes, exceptionally large structures taking even longer). You don't need to keep the tab open to access your results, as long as you copy the link shown on the page. When the calculation is finished, you will be redirected to the results subpage.
In the results page you can view a structure that has been analysed with Voronoia. You can see a view box in the middle of the page, where the structure is shown as well as an array of balls with different sizes. These balls represent cavities in the structure, which could potentially hold water molecules. Blue balls indicate polar cavities, which have a higher probability of containing water molecules, red balls on the other hand represent cavities which are mostly hydrophobic and therefor less likely to hold water molecules. The atoms surrounding cavities are highlighted, allowing you to investigate the cavities on your own.
The structure is colored by the packing density of the atoms, with red representing areas of low packing density and high flexibiliy, white showing average values of packing density and blue color indicating exceptionally rigid regions of the structure. Intermediate values are colored as mixed shades.
If you want to examine the structure in a bigger view box you can click on the fullscreen icon located under the view box on the right.
You can also download the results as a zip file on the results subpage by clicking on the download icon under the view box. The zip file contains a vor.pdb file, an holes.pdb file as well as a neighbors.pdb file which contains all atoms neighbouring cavities.
When you download the results for the structure you wish to analyse, you will find three files: protein.vor.pdb, protein_holes.pdb and protein_neighbors.pdb. protein.vor.pdb is a PDB file with some additional information generated by Voronoia: every ATOM-line in the original PDB is extended by the van der Waals-volume of the atom, the solvent excluded volume of the atom and a bit (a zero or a one), which shows whether the atom is solvent accesible (1) or burried in other atoms with no surface which the solvent can reach (0).
protein_holes.pdb is a pdb file that stores the position as well as approximate radius of every cavity that Voronoia calculated. The cavities are stored as hydrogen atoms in the PDB, with the B-Factor storing the radius in Angstrom. Storing the information in a PDB-file allows for the visualisation of the cavities in programs that are designed for the visualisation of PDB structures. The Polarity of the cavity is stored in the occupancy column.
The protein_neighbors.pdb file contains all atoms that neighbor cavities. By examining these atoms one can better determine the probability of a water molecule residing in a particular cavity.
Thank you for using Voronoia!