Swiss-PdbViewer is aimed at becoming a protein analysis and modelling workbench, tightly linked with the SWISS-model server [1]. In the current development state, Swiss-PdbViewer allows one to load up to ten PDB files simultaneously. Related proteins can then automatically be fitted in 3D space with a single command (using SIM [2] to find the best local alignment among target and reference proteins. Selected amino-acids are then subsequently used as a starting point for a least square fit).
A multiple alignment window offers a convenient way to look at conserved amino-acids, with various colouring options (RMS from reference protein, amino-acid kind, B-factor, secondary structures). As the user moves the cursor over aligned amino-acids, a visual feedback is provided in the 3D-view window, where the corresponding residues flash, which allows to rapidly focus on regions of interest.
A very intuitive graphic and menu driven interface provides access to various analysis features such as Ramachandran plots [3]; tools to measure distances, angles, and torsions angles; tools to evaluate H-bonds (even when explicit hydrogens are not present) or to mutate amino-acid side chains (by browsing a rotamer library [4]). During the mutation process, the best rotamer is directly suggested and H-bonds and steric hindrances are automatically estimated and displayed in real time, facilitating the best rotamer choice.
A control Panel regroups all of the most frequently used display facilities so that display/undisplay of individual aminoacids sidechain, van der Waals dots surface, color, and atom types and names (according to [5]), are accessible with a single click. Views can then be exported as Pdb files, images, or POV [6] scenes descriptions for Ray-tracing rendering.
The program is under constant improvement and can be retrieved freely by anonymous FTP from ExPASy [7].