Paper Citing NAMD - Abstract
Shih, Amy Y.; Sligar, Stephen G.; Schulten, Klaus
Molecular models need to be tested: The case of a solar flares discoidal HDL model
BIOPHYSICAL JOURNAL, 94:L87-L89, JUN 15 2008
In the absence of atomic structures of high-density lipoproteins in their lipid-bound states, many molecular models have been produced based on experimental data. Using molecular dynamics, we show that a recently proposed "solar-flares" model of discoidal high-density lipoprotein is implausible. Our simulations show a collapse of the protruding solar-flare loops and a notable protein rearrangement due to an energetically unfavorable orientation of the hydrophobic protein surface toward the aqueous solvent.
DOI:10.1529/biophysj.108.131581
