PMC:1867812 / 5124-5983 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1867812","sourcedb":"PMC","sourceid":"1867812","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1867812","text":"Clearly, protein folding trajectories consist of both spatial and temporal components. Each protein in a MD simulation is composed of a number of residues spatially located in the 3D space that move over time. Each frame (or snapshot) of the trajectory can be represented as a 2D contact map, which captures the pair-wise 3D distances between residues. We extract non-local bit-patterns from these contact maps. We then use an entropy-based clustering algorithm to cluster such bit-patterns into groups. These bit-patterns are further associated to form spatial object association patterns (SOAPs). By using SOAPs, we are able to effectively summarize and analyze folding trajectories produced by MD simulations. A major advantage of this representation is its appropriateness for cross-comparison across different simulations, as discussed in later sections.","tracks":[]}