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BMCBI
2010

Fast and accurate protein substructure searching with simulated annealing and GPUs

9 years 10 months ago
Fast and accurate protein substructure searching with simulated annealing and GPUs
Background: Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif) searching. Results: We developed an improved heuristic for tableau-based protein structure and substructure searching using simulated annealing, that is as fast or faster and comparable in accuracy, with some widely used existing methods. Furthermore, we created a parallel implementation on a modern graphics processing unit (GPU). Conclusions: The GPU implementation achieves up to 34 times speedup over the CPU implementation of tableaubased structure search with simulated annealing, making it one of the fastest available methods. To the best of our knowledge, this is the first application of a GPU to the protei...
Alex Stivala, Peter J. Stuckey, Anthony Wirth
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Alex Stivala, Peter J. Stuckey, Anthony Wirth
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