Interactive Exploration of Protein Cavities

• Published in: Computer graphics forum 2011-06, Vol.30 (3), p.673-682
• Main Authors: Krone, M., Falk, M., Rehm, S., Pleiss, J., Ertl, T.
• Format: Article
• Language: English
• Subjects: Analysis; Binding sites; Biology and Genetics I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling; Boundary Representations I.4.6 [Image Processing and Computer Vision]: Segmentation; Channels; Computer graphics; Datasets; Exploration; Holes; Image processing systems; Interactive; J.3 [Computer Applications]: Life and Medical Sciences; Molecular structure; particles; Proteins; Region Growing; Segmentation; Studies; Trajectories; volume
• ISSN: 0167-7055; 1467-8659; 1467-8659
• DOI: 10.1111/j.1467-8659.2011.01916.x

We present a novel application for the interactive exploration of cavities within proteins in dynamic data sets. Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens up to the environment, making the binding site accessible to the surrounding substrate. Our user‐driven approach enables expert users to select a certain cavity and track its evolution over time. The user is supported by different visualizations of the extracted cavity to facilitate the analysis. The boundary of the protein and its cavities is obtained by means of volume ray casting, where the volume is computed in real‐time for each frame, therefore allowing the examination of time‐dependent data sets. A fast, partial segmentation of the volume is applied to obtain the selected cavity and trace it over time. Domain experts found our method useful when they applied it exemplarily on two trajectories of lipases from Rhizomucor miehei and Candida antarctica. In both data sets cavities near the active center were easily identified and tracked over time until they reached the surface and formed an open substrate channel.