Protein molecular viewer – the visualization of protein molecular structures stored in the PDBML format

Abstract

Visualization of protein molecular structures is a very important part of the analysis of protein function and activity. Molecular viewers allow to represent graphically the complex construction of proteins and give us an idea of the biological molecules built up with hundreds or thousands of atoms linked to each other by covalent bonds. In the chapter we present the most interesting features of our Protein Molecular Viewer (PMV). PMV is a mo­le­cular visualization tool developed at the Silesian University of Technology in Gliwice, which is used to show protein structures loaded from the well-known Protein Data Bank. With the possibility of loading and presenting protein structures from the PDBML data format the PMV becomes one of a few tools in the world having this unique function.