Sirius is designed as a desktop environment that covers most of essential operations that are needed to visualize structures of proteins and small molecules, as well as to carry out analyses, comparisons and data mining.

Sirius has three main components for data visualization: molecular graphics component (3D viewer), Sequence Viewer and Structure Browser. They share a common event scheme, which means that any selection or coloring change in one of them is automatically reflected in the others. For example, coloring of a sequence alignment by side chain conservation while a representative structure is loaded will immediately show which regions of the structure are conserved.

While the default 3D viewer displays three-dimensional structures, Structure Browser panel shows the hierarchical structure of the data: chains, residues and atoms of the loaded structures. It can be used for easy navigation, since it's frequently more convenient to find a specific atom or residue in the list rather than in the structure. Structure Browser also features context-specific menus and information display panel.

Sequence viewer displays primary sequences of proteins and DNA. Small molecules are displayed here as well, however, they are shown as # symbols to denote non-protein monomers. Selection and coloring between viewers works equally well for both types of data.

In addition to shared event scheme, the connection between the components is also interactive. If a structure in the 3D component is modified (e.g., amino acid is replaced or deleted, or a small molecule is built from two fragments), sequence viewer reflects the change by updating the sequence and its properties. A Ramachandran plot can be generated for protein sequences, and it offers the same degree of interactivity. In addition to shared selection and coloring, any change to the phi/psi angles in the structure is displayed in the position change of the residue marker as the change progresses.