PocketQuery Help

PocketQuery is a web interface for exploring the the properties of protein-protein interaction (PPI) interfaces with a focus on the discovery of promising starting points for small-molecule design. PocketQuery is regularly updated with PPI structures from the PDB. All protein-containing complexes are analyzed using the first biological assembly. If a biological assembly is not available, the first model of the asymmetric unit is used. Additionally, users may upload their own PPI structures.

A cluster of 6 residues at the p53/MDM2 interface (PDB: 1YCR).


Because of the focus on identifying small-molecule starting points, the primary unit of analysis in PocketQuery is a cluster of interface residues. An interface residue is defined as a residue where the change in SASA upon complexation is more than 0.05Å2. Only clusters where the maximum distance between the center of mass of any two residues is less than 12Å are analyzed. Only standard residues are analyzed (modified residues are removed from the structure).
Properties of residue clusters that can be used as search criteria.


Each cluster of residues is annotated with a large collection of pre-computed properties. Per-residue properties, such as the change in solvent accessible surface area (SASA), are aggregated into lowest, highest, average, and total values for the cluster.


All of the above properties can be used as search criteria to find clusters of residues. The Add Search Criteria button allows you to conjunctively combine an arbitrary number of filters to create a highly specific custom filter. Filter presets are also available (bottom left) for common categories. Both the lower and upper bounds of value ranges are inclusive (e.g., a cluster size filter between 3 and 4 will return all clusters of size 3 and 4). If a value is left unspecified, then the range is open-ended.

The Load and Save buttons in the Search panel allow the saving and sharing of specific sets of search criteria. An example search for the p53/MDM2 interface can be performed here.

Browsing Results

The Clusters panel displays all the matching clusters of the specified search. Because there are a large number of properties associated with each cluster, there are multiple viewing options that display different subsets of properties. For example, Cluster Averages displays the PDB, chain (Ch), number of residues in the cluster (Sz), maximum spanning distance of the cluster (Dist), average energy and SASA properties, and the overall score. The Residue Centric view (see below) provides the PDB, chain, residue type, residue number, and total energy and SASA properties. The clusters may be sorted by any shown property by clicking the corresponding column header. The direction of sort can be changed by clicking the column header a second time.

Selecting a cluster row will create a WebMol viewer of the selected cluster (left panel). If your browser supports WebGL, a WebGL viewer based off of GLmol will be used, otherwise the Jmol viewer will be used and Java will be required. The controls for these viewers are shown below.

WebGL ViewerJmol Viewer
RotateLeft clickLeft click
TranslateCtrl-click or middle clickCtrl-right click or Shift-double click
ZoomScroll wheel, Shift-click, or right clickScroll wheel or Shift-click

Multiple clusters on the same chain may be selected using the Shift or Cntrl keys (see below). Details on the individual residues of the cluster are shown in the Residues tab beneath the molecular viewer. Selecting individual residues in this table will highlight the corresponding residue in the viewer (see above).


The Viewer tab under the molecular viewer controls the display of the protein-protein interface. The receptor protein consists of all chains of the complex that are not the cluster chain. The transparency of the receptor surface can be scaled from fully opaque to completely absent. The receptor surface is color mapped to the partial charges of the residues. There are several residue styles to choose from to display the receptor and ligand protein residues.

The ligand protein is the full chain of the selected cluster(s), including non-interface residues. Residues belonging to the selected cluster(s) are display in a separate style specified by Cluster Style.

Interface residues may be colored by their property values, such as ΔG. Properties are mapped to a rainbow (ROYGB) spectrum where the smallest values are always red and the largest blue.

Saving Results

Options for exporting the structure of selected cluster(s).
The numerical properties of all the clusters matching a search may be saved as a text file using the Save Results button in the Clusters panel. If you are interested in performing a system-wide analysis of the data, please contact us for direct access to the underlying database rather than attempting to download the hundreds of gigabytes of data in plain text.

The structure of the selected cluster(s) shown in the molecular viewer may be exported for further analysis. The cluster may be saved as a PDB file or the structure can be sent to either the AnchorQuery or ZINCPharmer websites. These pharmacophore search engines will automatically identify a candidate interaction pharmacophore from the exported cluster.

Citing PocketQuery

The underlying methodology of PocketQuery is described in our article in Bioinformatics while the webserver is described in the 2012 webserver issue of Nucleic Acids Research. If you make use of the score feature, please give citation priority to the Bioinformatics article.

Data Access

If you would like direct access to the underlying MySQL database, please email David Koes. The supporting information for our Bioinformatics paper, including the source code to our exhaustive rule learner, can be found here.