An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories

Background: Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data. Hence there is a pressing need to be able to interpret and identify novel folding features from them. Results: In this paper, we model each folding trajectory as a multi-dimensional curve. We then develop an effective multiple curve comparison (MCC) algorithm, called the enhanced partial order (EPO) algorithm, to extract features from a set of diverse folding trajectories, including both successful and unsuccessful simulation runs. The EPO algorithm addresses several new challenges presented by comparing high dimensional curves coming from folding trajectories. A detailed case study on miniprotein Trp-cage [1] demonstrates that our algorithm can detect similarities at rather low level, and extract biologically meaningful folding events. Conclusion: The EPO algorithm...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Hong Sun, Hakan Ferhatosmanoglu, Motonori Ota, Yusu Wang
• Keywords: Algorithm, BMCBI 2008, Folding Simulations, Protein