User guide

PrankWeb is a web-based application that allows to predict and visualize protein-ligand binding sites. Furthermore, it allows to compare the location of predicted pockets with highly conserved areas as well as actual ligand binding sites. All one needs to use PrankWeb is a device with a web-browser that supports WebGL.

Specify what protein to analyze

There are two options to analyze a protein:

Homology

Besides selecting what protein to analyze, one can also specify whether evolutionary conservation should be included in the prediction model by checking the Run conservation analysis checkbox. Note that calculating conservation score for user-defined protein file can significantly increase the time of analysis unless you specify its PDB identification code or upload multiplesequence alignments for homology calculation.

There are three ways how to calculate the conservation score for the protein:

Visualization

Once the protein visualization is loaded, three main panels appear: sequence visualization, structural visualization and the pocket panel.

Structural visualization

The largest panel contains the three-dimensional visualization of the protein.

Controls

The molecule can be rotated by moving mouse while holding left mouse button. On a touch device, just slide your finger. To zoom in or out, move your mouse while holding the right mouse button or use the pinch gesture on a touch display. In order to move the protein, do the same, but this time hold the wheel button. Lastly, for slabbing the protein, scroll the mouse wheel or use the three finger gesture.

Using the buttons in the top-right corner, one can:

By toggling the advanced control panel, one has full control over the content of the visualization using LiteMol. For more help with LiteMol, please visit its wiki page .

Sequence visualization

The panel above protein 3D visualization displays protein sequence.

As one hovers over the sequence with mouse, the residues are highlighted in the 3D visualization. This feature allows to analyze the protein both from the structural and sequential point of view. By default, the sequence view is zoomed out so that the whole protein is displayed. You can use the trackbar control to zoom in, or select the area with mouse and zoom to the selection. A snapshot of the sequence can be captured and exported to SVG (Scalable Vector Graphics) file using the rightmost button.

Pocket panel

The right panel contains several control buttons and a list of predicted pockets. Use the control buttons to download PrankWeb report, hide the sequence view or switch between the structural views. In the pocket list, pocket name, rank, size and average conservation score (if available) is displayed for each pocket. Each pocket also contains several buttons related to visibility of the pockets in the visualizations.

Contact us

Something is not working or are you missing certain functionality/feature? Please let us know by creating a GitHub issue . Alternatively, if you prefer to use email, please feel free to reach us at david.hoksza (at) mff.cuni.cz.


PrankWeb is a part of services provided by ELIXIR – European research infrastructure for biological information.
See services provided ELIXIR's Czech Republic Node .

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