title: Diffusion accessibility as a method for visualizing macromolecular surface geometry.
abstract: Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles.
authors.forename: Yingssu
authors.initials: Y
authors.lastname: Tsai
authors.affiliation: UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Holton
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles.|UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA.
authors.forename: Todd O
authors.initials: TO
authors.lastname: Yeates
mesh_terms: D004058:Diffusion; D046911:Macromolecular Substances; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D046911:Macromolecular Substances; D011506:Proteins
keywords: Laplace; Poisson-Boltzmann; binding sites; computer graphics; protein surfaces; surface curvature