Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A generalized framework for mining spatio-temporal patterns in scientific data
Proceedings of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
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Molecular Dynamics-based simulations have been employed to study the protein folding process, in which a protein acquires its functional three-dimensional structure. This has resulted in a large number of protein folding trajectories. As a result, it becomes increasingly important to analyze such data to facilitate a deeper understanding of the protein folding mechanism. In this paper, we focus on identifying important 3D structural motifs in the folding data. We have proposed a multi-step algorithm that is not only computationally efficient but also captures the evolving nature of the folding process. Empirical evaluation demonstrates that such motifs are effective at characterizing a protein's structural evolution in its folding process. We also show that such motifs can be utilized to address important folding issues such as detecting important folding events, and structurally characterizing a folding pathway.