Protein Structure Prediction on GPU: A Declarative Approach in a Multi-agent Framework

This paper provides a novel perspective in the Protein Structure Prediction (PSP) problem. The PSP problem focuses on determining putative 3D structures of a protein starting from its primary sequence. The proposed approach relies on a multi-agents approach, where concurrent agents explore the folding of different parts of a protein. The strength of the approach lies in the agents´ ability to apply different types of knowledge (expressed in the form of declarative constraints) to prune the local space of folding alternatives. The paper demonstrates the suitability of a GPU approach to implement such multi-agent infrastructure, with significant improvements in speed and quality of solutions w.r.t. other methods (e.g., based on fragments assembly approaches).