posted on 2017-02-14, 00:00authored byBrooke
E. Husic, Vijay S. Pande
Markov state models (MSMs) are a
powerful framework for analyzing
protein dynamics. MSMs require the decomposition of conformation space
into states via clustering, which can be cross-validated when a prediction
method is available for the clustering method. We present an algorithm
for predicting cluster assignments of new data points with Ward’s
minimum variance method. We then show that clustering with Ward’s
method produces better or equivalent cross-validated MSMs for protein
folding than other clustering algorithms.