Hierarchical Extended Linkage Method (HELM)'s Deep Dive into Hybrid Clustering Strategies.

ABSTRACT: Clustering remains a key tool in the analysis of molecular dynamics (MD) simulations, from the preparation of kinetic models to the study of mechanistic pathways and structural determination. It is no surprise then that multiple algorithms are currently used in the MD community, with k -means and hierarchical approaches being arguably the two most popular approaches. The former is very attractive from a purely computational point of view, demanding minimal memory and time resources, but at the price of being able to partition the data in very restrictive ways. Hierarchical strategies, on the other hand, can generate arbitrary partitions, but with steep memory and time requirements due to their need to build a pairwise distance matrix for all the considered conformations/frames. Here we pro

SUBMITTER: Chen L 

PROVIDER: S-EPMC11952300 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature