University of Missouri researchers have developed an algorithm, called ppsAlign, which is a high-performance protein structural alignment tool designed to tackle the computational complexity issues from protein structural data. Results have indicated a many-fold increase in speed over other highly touted alignment algorithms, while maintaining comparable or better quality in all cases.
Large-scale protein structural alignment, an indispensable tool to life sciences and pharmaceutical industry, poses a tremendous challenge on computational resources. To ensure structural alignment accuracy and efficiency, other research attempts to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and are of limited accessibility. Others trade alignment quality for speed by using high-level characteristics of structure fragments for structure comparisons. An inexpensive, accurate, and speedy algorithm is needed to handle the ever-growing size of protein structures.
This algorithm uses a parallel protein structural alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs).
POTENTIAL AREAS OF APPLICATIONS:
MAIN ADVANTAGES OF INVENTION:
-Implements structural alignment at the residue level
-Parallel computing framework
-Efficient organization of memory layout and retrieval
STATE OF DEVELOPMENT:
-Ready to be commercialized