GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences

Publisher Summary This chapter describes the new version of Graphical Representation and Analysis of Surface Properties (GRASP), which contains many new capabilities. The widespread use of the original version of GRASP revealed the importance of the visualization of physicochemical and structural properties on the molecular surface. The GRASP program was written a number of years ago; it was the first program specifically designed to display the molecular surface. It also provided several unique analytical tools. For example, electrostatic potentials calculated using the finite-difference Poisson–Boltzmann (FDPB) method could be displayed on the molecular surface. The new version of GRASP has been written using the object-oriented programming language C++, making the algorithms and code easily accessible and modifiable. Also, molecular graphics functionality is carried out using the platform-independent graphics language OpenGL, making it more portable (GRASP2 currently runs on PCs running Microsoft Windows). The surface of a biological macromolecule is the region of the structure with which other molecules can interact. Consequently, the visualization and analysis of surface properties can contribute significantly to the understanding of the physical determinants of protein function, from chemical catalysis to allosteric properties to protein–protein, protein–ligand, and protein–membrane interactions.