Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories.

ABSTRACT: Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods have focused on the use of internal coordinates due to the innate rotational and translational invariance of these features. The vast number of possible internal coordinates necessitates a feature space supervision step to make clustering tractable but yields a protocol that can be system type-specific. Particle positions offer an appealing alternative to internal coordinates but suffer from a lack of rotational and translational invariance, as well as a perceived insensitivity to regions of structural dissimilarity. Here, we present a method, denoted shape-GMM, that overcomes the shortcomings of particle positions

SUBMITTER: Klem H 

PROVIDER: S-EPMC9228201 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature