F2Dock: fast Fourier protein-protein docking.

The functions of proteins are often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination, and understanding function and structure relationships. In this paper, we extend our nonuniform fast Fourier transform-based docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, F2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .

VIPERdb: a relational database for structural virology.

VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.

Compressed representations of macromolecular structures and properties.

We introduce a new and unified, compressed volumetric representation for macromolecular structures at varying feature resolutions, as well as for many computed associated properties. Important caveats of this compressed representation are fast random data access and decompression operations. Many computational tasks for manipulating large structures, including those requiring interactivity such as real-time visualization, are greatly enhanced by utilizing this compact representation. The compression scheme is obtained by using a custom designed hierarchical wavelet basis construction. Due to the continuity offered by these wavelets, we retain very good accuracy of molecular surfaces, at very high compression ratios, for macromolecular structures at multiple resolutions.

Volumetric Video Compression for Interactive Playback.

We develop a volumetric video system which supports interactive browsing of compressed time-varying volumetric features (significant isosurfaces and interval volumes). Since the size of even one volumetric frame in a time-varying 3D data set is very large, transmission and on-line reconstruction are the main bottlenecks for interactive remote visualization of time-varying volume and surface data. We describe a compression scheme for encoding time-varying volumetric features in a unified way, which allows for on-line reconstruction and rendering. To increase the run-time decompression speed and compression ratio, we decompose the volume into small blocks and encode only the significant blocks that contribute to the isosurfaces and interval volumes. The results show that our compression scheme achieves high compression ratio with fast reconstruction, which is effective for client-side rendering of time-varying volumetric features.