期刊
PROTEIN SCIENCE
卷 24, 期 10, 页码 1702-1705出版社
WILEY-BLACKWELL
DOI: 10.1002/pro.2752
关键词
protein surfaces; Poisson-Boltzmann; surface curvature; computer graphics; binding sites; Laplace
资金
- BER program of the DOE Office of Science [DE-FC02-02ER63421]
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/.
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