Paper Citing NAMD - Abstract
Pietropaolo, Adriana; Branduardi, Davide; Bonomi, Massimiliano; Parrinello, Michele
A Chirality-Based Metrics for Free-Energy Calculations in Biomolecular Systems
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2627-2637, SEP 2011
In this work, we exploit the chirality index introduced in (Pietropaolo et al., Proteins 2008, 70, 667) as an effective descriptor of the secondary structure of proteins to explore their complex free-energy landscape. We use the chirality index as an alternative metrics in the path collective variables (PCVs) framework and we show in the prototypical case of the C-terminal domain of immunoglobulin binding protein GB1 that relevant configurations can be efficiently sampled in combination with well-tempered metadynamics. While the projections of the configurations found onto a variety of different descriptors are fully consistent with previously reported calculations, this approach provides a unifying perspective of the folding mechanism which was not possible using metadynamics with the previous formulation of PC Vs. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2627-2637, 2011
