Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions.

ABSTRACT: In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule are a direct representation of a macromolecular configuration, and yet, they are not used in enhanced sampling studies due to a lack of rotational and translational invariance. We resolve this issue using the technique of our prior work, whereby a molecular configuration is considered a member of an equivalence class in size-and-shape space, which is the set of all configurations that can be translated and rotated to a single point within a reference multivariate Gaussian distribution characterizing a single molecular state. The reaction coordinates produc

SUBMITTER: Sasmal S 

PROVIDER: S-EPMC10373481 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature