An automated protein structure prediction algorithm, pro-sp3-Threading/ASSEmbly/Refinement (TASSER), is described and benchmarked. Structural templates are identified using five different scoring functions derived from the previously developed threading methods PROSPECTOR_3 and SP(3). Top templates identified by each scoring function are combined to derive contact and distant restraints for sub...

Low precision arithmetic, in particular half (16-bit) floating point is now available commercial hardware. Using lower can offer significant savings computation and communication costs with proportional energy. Motivated by this, there has been a renewed interest mixed iterative refinement schemes for solving linear systems A x = b , new variants of GMRES-based have developed. Each variant give...

Malaria vaccination is an essential approach to combat malaria. One major protein studied for vaccine development Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1). It contains several important domains malaria pathogenesis. The binding of Cysteine-rich interdomain region ?1 (CIDR?1) PfEMP1 endothelial C receptor (EPCR) associated with cerebral malaria, while CIDR?1 CD36 has been co...

Despite considerable efforts to develop accurate template free approaches, template-based protein structure modeling is still the only reliable protein structure modeling method.1 Templatebased modeling involves (1) template identification, usually by threading; (2) construction of the target-template alignment; (3) model generation based on this alignment; and (4) refinement of the template mo...

The Schur decomposition of a square matrix A is an important intermediate step state-of-the-art numerical algorithms for addressing eigenvalue problems, functions, and equations. This work concerned with the following task: Compute (more) accurate from given approximate decomposition. task arises, example, in context parameter-dependent problems mixed precision computations. We have developed N...

The understanding of protein-protein interactions is a major goal in the postgenomic era. The prediction of interaction from sequence and the subsequent generation of full-length dimeric models is therefore of great interest especially because the number of structurally characterized protein-protein complexes is sparse. A quality assessment of a benchmark comprised of 170 weakly homologous dime...

This work introduces an iterative soft cluster refinement method that extensively uses soft cluster evaluation to determine which clusters would discriminate between classes in a classification scheme. This iterative refinement is part of the continuous iterative guided spectral class rejection (CIGSCR) classification method for remotely sensed images. Results indicate that CIGSCR produces good...

Perentie is a software analysis tool based on iterative refinement of trace abstraction: if the refinement process terminates, the program is either declared correct or a counterexample is provided and the program is incorrect.