CMPyMOL: A Tool for Protein Contact-Map Analysis

Abstract

Contact-maps are reduced 2D representation of the 3D spatial configuration of a protein. Many valuable structural features like secondary structures, inter- and intra-protein interactions,interacting domains, etc., can be readily identified from these maps. However, it is not straightforward and intuitive to reckon the spatial organization of the contact regions from reduced representation. The CMPyMOL extention for molecular visualization software PyMOL attempts to bridge this gap as an interactive graphical tool for protein contact-maps that interfaces with PyMOL for 3D visualization. Specifically, CMPyMOL helps understand the functional importance of contacts by providing visual overlays of various structural and biochemical properties of a protein on top of its contact-map.