Normal Mode Analysis is a fast and inexpensive approach that is largely
used to gain insight into functional protein motions, and more recently
to create conformations for further computational studies. However, when
the protein structure is unknown, the use of computational models is
necessary. Here, we analyze the capacity of normal mode analysis in
internal coordinate space to predict protein motion, its intrinsic
flexibility and atomic displacements, using protein models instead of
native structures, and the possibility to use it for model refinement.
Our results show that normal mode analysis is quite insensitive to
modelling errors, but that calculations are strictly reliable only for
very accurate models. Our study also suggests that internal normal mode
analysis is a more suitable tool for the improvement of structural
models, and for integrating them with experimental data or in other
computational techniques, such as protein docking or more refined
molecular dynamics simulations.