Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


Exploring protein energy landscapes with hierarchical clustering


International Journal of Quantum Chemistry, 105:826–830, 2005


In this work we present a new method for investigating local energy minima on a protein energy landscape. The CABS (CAlpha, CBeta and the center of mass of the Side chain) method was employed for generating protein models, but any other method could be used instead. Cα traces from an ensemble of models are hierarchical clustered with the HCPM (Hierarchical Clustering of Protein Models) method. The efficiency of this method for sampling and analyzing energy landscapes is shown.