Docking scores, predicted binding affinities for target proteins, are displayed in an interactive table and histogram (Figure 1C). By clicking on a table entry or histogram bar, molecular binding interactions can be graphically displayed in 2D/3D for structure-based investigation. Analyzed by LIGPLOT (35 (link)), protein residues involved in intermolecular interactions will be highlighted for rapid inspection. Screening result files from systemsDock are rich in details. Tabulated docking scores (csv file), docked poses (SDF file), processed protein structures (PDB file), and predicted binding interactions (png file) may be downloaded. The pathway map (SBML file, svg/png file), if available, may be saved. Depending upon availability of the pathway map, docking scores of the test compound against specified network proteins are optionally converted into a white-to-red color scale (indicating binding strength) or they may be classified as active (red) or inactive (white) relative to a specified cutoff. Colored results are then projected to the pathway map to directly display predicted binding affinities (Figure 1D). For larger data visualization and analysis, an interactive heat map with sorting and zooming functions is also available for users (Figure 1E), through which users can efficiently identify potential binders or known targets from plenty of tests.
systemsDock provides a set of efficient functions to manipulate the pathway map. For example, a bird's-eye-view function facilitates navigating over a pathway map. An object-list panel lists object information (e.g. species, proteins and reactions) shown on the map. Then, by simply by clicking on an entry one can center and highlight the object in the view. Users can efficiently investigate the bioactivity of a test compound against numerous proteins through the colored pathway, allowing a perspective inspection for results throughout a complex signaling network. By clicking on colored nodes (proteins), a molecule visualizer (JSmol) will be launched to illustrate the intermolecular interactions in 2D/3D (Figure 1F). Screening results are retrievable by a given web link or session ID. There is no login requirement to use systemsDock, but historical sessions and results may be retrieved and managed after login verification.