Fast and accurate protein substructure searching with simulated annealing and GPUs

Fast and accurate protein substructure searching with simulated annealing and GPUs

Blog Article

Abstract Background Searching a database of protein structures for matches to a query structure, or occurrences of OPTIONS_HIDDEN_PRODUCT 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 tableau-based structure search with simulated annealing, Inbound making it one of the fastest available methods.To the best of our knowledge, this is the first application of a GPU to the protein structural search problem.