Paper Citing NAMD - Abstract
Banu, Mihaela; Patriche, Simona; Coman, Malina; Matsushita, S.; Tofan, Alice; Epureanu, A.
Investigation of ubiquitin deformation mechanism under induced stretch-compression loads
ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY, 52:449-454, 2011
Proteins folding and unfolding are conformational changes in the life of the proteins, which reveal the modifications in the organization of the molecules inside the chain. It is known that a very organized structure has great amount of entropy and tends to exchange the energy with the environment. The present work presents the results of the atomistic modeling using NAMD software released by the University of Illinois, USA, to reveal the hyper-elasticity under external loads and the progressive conformational shapes that are produced by the H-bonds breaking and recovering. Each H-bond break produces a leap in the internal energy, probably by influencing the bond-bind energy component of the internal energy.
