Paper Citing NAMD - Abstract
Cotallo-Aban, M.; Prada-Gracia, D.; Mazo, J. J.; Bruscolini, P.; Falo, F.; Sancho, J.
Analysis of apoflavodoxin folding behavior with elastic network models
FROM PHYSICS TO BIOLOGY: THE INTERFACE BETWEEN EXPERIMENT AND COMPUTATION, 851:135-149, 2006
We apply simple elastic network models to study some properties of the unfolding of apoflavodoxin, a protein that shows a three-state thermodynamic behavior under thermal denaturation, as revealed by extensive analysis of wildtype and mutant variants. The intermediate of apoflavodoxin presents an overall structured core, with just a part of the protein being substantially unfolded [1]. In agreement with these results, we have been able to identify, using different models and methods, the more mobile regions in the thermal unfolding of the protein. We also discuss how the predictions obtained from these models could help in designing new experiments.
