BioGem Blog

This tutorial presents various models of molecular graphics representations such as Wireframe model, Ball & Stick model, Spacefill model, Surface model, Stick model, Backbone model, Van der Waals model, Ribbon model, Strand model, and Electrostatic potential model of protein structure using Swiss PDB Viewer . Protocol Open Swiss PDB Viewer software. Click File → Open PDB File… menu to browse protein structure (. pdb file) location. By default, it displays protein structure in “ Wireframe ” model. In Control Panel window, right-click symbol “ ::v ” to display whole protein structure in “ Van der Waals ” model. Click Display → Render in Solid 3D menu, and click Display → Show Backbone Oxygens menu (deselect) to display protein structure in “ Sticks ” model. In Control Panel window, right-click symbol “ side ” to display whole protein structure in “ Backbone ” model. In Con...

DeepView – Swiss-PdbViewer (or SPDBV) is an bioinformatics application that provides a user friendly graphical interface allowing to view and analyze protein and nucleic acid structure. This program is associated with Swiss-Model (an automated homology modeling server running in the Geneva Glaxo Welcome Experimental Research), accessible via the ExPASy web server. Through this application, proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and ...