Vinay Siddavanahalli

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While molecular visualization software has advanced over the years, today, most tools still operate on individual molecular structures with limited facility to manipulate large multi-component complexes. We approach this problem by extending 3D image-based rendering via programmable graphics units, resulting in an order of magnitude speedup over traditional(More)
We present an adaptive grid based algorithm to compute a family of relevant molecular surfaces. Molecular interfaces are important in simulations and visualization involving biomolecules. The Richards surface has traditionally been used as a good approximation to the surface, and defined as the surface formed by the inner facing part of a solvent probe atom(More)
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(More)
Volumetric smooth particle data arise as atomic coordinates with electron density kernels for molecular structures, as well as fluid particle coordinates with a smoothing kernel in hydrodynamic flow simulations. In each case there is the need for efficiently computing approximations of relevant surfaces (molecular surfaces, material interfaces, shock waves,(More)
In this paper, we describe a compression scheme for encoding time-varying isosurfaces and amorphous volumetric features (volumes within specified value ranges) in a unified way, which allows for on-line reconstruction and rendering. Since the size of even one frame in a time-varying data set is very large, transmission and on-line reconstruction are the(More)
Adaptive mesh refinement (AMR) is a popular computational simulation technique used in various scientific and engineering fields. Although AMR data is organized in a hierarchical multi-resolution data structure, the traditional volume visualization algorithms such as ray-casting and splatting cannot handle the form without converting it to a sophisticated(More)
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,(More)
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(More)
While molecular visualization software has advanced over the years, today, most tools still operate on individual molecular structures with little facility to manipulate large multi-component complexes, or depict molecular flexibility. We extend and accelerate 3D image-based rendering via programmable graphics units to provide an order of magnitude speedup(More)
Abstract Protein interactions, key to many biological processes, involves induced fit between flexible proteins which typically undergo conformational changes. Modeling this flexible protein-protein docking is an important step in drug discovery, structure determination and understanding structure-function relationships. In this paper, we present F3Dock, a(More)