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

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 <i>k</i>-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 propose a new hybrid paradigm, the hierarchical extended linkage method (HELM), that retains the efficiency of <i>k</i>-means while incorporating the flexibility of hierarchical methods. The key ingredient is the use of <i>n</i>-ary difference functions as a way to stabilize the <i>k</i>-means results and efficiently build the hierarchy of subsets. We showcase the applicability of this strategy over protein-DNA and protein folding studies, including the complete analysis of simulations with over 1.5 million frames. HELM is freely available in our MDANCE clustering package.