2.3 Folding Trajectory Analysis: Objectives
There are two main goals we would like to achieve in analyzing the folding trajectories. First, we would like to address the following issues for individual trajectories: (1) to detect (or predict) significant folding events, including the formation of β-turns, α-helices, and native-like conformations; and (2) to recognize the temporal ordering of important folding events in the trajectory. For instance, between the two secondary structures α-helix and β-hairpin in BBA5, which forms earlier? What is ordering of the two events preceding a β-hairpin formation: formation of two extended strands or formation of the turn?
In contrast to the first goal, our second goal concerns multiple trajectories. Specifically, we would like to identify a sub-sequence of similar conformations across trajectories. This sub-sequence of conformations is referred to as the consensus partial folding pathway. This is analogous to the Longest Common Sub-sequence (LCS) problem [17], but much more challenging due to the following reasons. First, we are dealing with time series of 3D protein structures. Second, we are looking for similar conformations across trajectories, and our work on mining spatio-temporal data [5].