Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

ABSTRACT: Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational ge

SUBMITTER: Seyler SL 

PROVIDER: S-EPMC4619321 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature