Thorough validation of protein normal mode analysis: a comparative study with essential dynamics

Structure. 2007 May;15(5):565-75. doi: 10.1016/j.str.2007.03.013.


The deformation patterns of a large set of representative proteins determined by essential dynamics extracted from atomistic simulations and coarse-grained normal mode analysis are compared. Our analysis shows that the deformational space obtained with both approaches is quite similar when taking into account a representative number of modes. The results provide not only a comprehensive validation of the use of a low-frequency modal spectrum to describe protein flexibility, but also a complete picture of normal mode limitations.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Computer Simulation*
  • Models, Chemical*
  • Normal Distribution
  • Proteins / chemistry*
  • Thermodynamics*


  • Proteins