MPlot-a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins

Abstract

MPlot is a webserver that provides a quick and easy way for structural biologists to analyze, visualize and plot tertiary structure contacts of helical membrane proteins. As input, experimentally determined or computationally modeled protein structures in PDB format are required. The automat-ic analysis concatenates in house tools to calculate cut-off dependent van der Waals contacts or crossing angles of transmembrane helices with third party tools to compute main chain or side chain hydrogen bonds or membrane planes. Moreover, MPlot allows new features and tools to be added on a regular basis. For that purpose, MPlot was embedded in a framework that facilitates advanced users to compose new workflows from existing tools, or to substitute intermediate results with results from their (own) tools. The outputs can be viewed online in a Jmol based protein viewer, or via automatically generated scripts in PyMOL. For further illustration, the results can be downloaded as a 2D graph, representing the spatial arrangement of transmembrane helices true to scale. For analysis and statistics, all results can be downloaded as text files that may serve as inputs for or as standard data to validate the output of knowledge based tertiary structure prediction tools. URL: http://proteinformatics.charite.de/mplot/. © The Author(s) 2010. Published by Oxford University Press.