We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading templates guided by a reduced Calpha and side-chain based potential consistent with threading based tertiary restraints. Predictions were generated for 745 proteins 201-300 residues in length that cover th...

We have developed TASSER, a hierarchical approach to protein structure prediction that consists of template identification by threading, followed by tertiary structure assembly via the rearrangement of continuous template fragments guided by an optimized C(alpha) and side-chain-based potential driven by threading-based, predicted tertiary restraints. TASSER was applied to a comprehensive benchm...

For appropriate matrix ensembles, greedy algorithms have proven to be an efficient means of solving the combinatorial optimization problem associated with compressed sensing. This paper describes an implementation for graphics processing units (GPU) of hard thresholding, iterative hard thresholding, normalized iterative hard thresholding, hard thresholding pursuit, and a two-stage thresholding ...

Query refinement is one of the main approaches for overcoming natural language lexical ambiguity and improving the quality of search results in Information Retrieval. In this paper we propose a knowledge–rich personalized approach for iterative query reformulation before sending it to search engines and entropybased approach for refinement quality estimation. The underling hypothesis is that th...

We adopt parallel computing and adaptive mesh refinement in a class of iterative inverse solution strategies for tomographic surveys. Due to the algorithmic structure of these inverse solvers, a combination of data parallelism and task parallelism is best suited. Targeting clusters of multicore processor chips, it also justifies to use a mixture of message passing and threads. Moreover, adaptiv...