2D depiction of nonbonding interactions for protein complexes

Abstract A program called the 2D‐GraLab is described for automatically generating schematic representation of nonbonding interactions across the protein binding interfaces. The input file of this program takes the standard PDB format, and the outputs are two‐dimensional PostScript diagrams giving intuitive and informative description of the protein–protein interactions and their energetics properties, including hydrogen bond, salt bridge, van der Waals interaction, hydrophobic contact, π–π stacking, disulfide bond, desolvation effect, and loss of conformational entropy. To ensure these interaction information are determined accurately and reliably, methods and standalone programs employed in the 2D‐GraLab are all widely used in the chemistry and biology community. The generated diagrams allow intuitive visualization of the interaction mode and binding specificity between two subunits in protein complexes, and by providing information on nonbonding energetics and geometric characteristics, the program offers the possibility of comparing different protein binding profiles in a detailed, objective, and quantitative manner. We expect that this 2D molecular graphics tool could be useful for the experimentalists and theoreticians interested in protein structure and protein engineering. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009