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Chemistry & biology 13 (6), 625-36 (Jun 2006)
Archives of biochemistry and biophysics 426 (2), 231-40 (15 Jun 2004)
Protein engineering 16 (2), 147-56 (Feb 2003)
Journal of molecular biology 359 (4), 876-89 (16 Jun 2006)
Metabolic engineering 7 (1), 18-26 (Jan 2005)
Physical Review Letters 77 (9), 1905 (1996)
Normal mode analysis (NMA) is a leading method for studying long-time dynamics and elasticity
of biomolecules. The method proceeds from complex semiempirical potentials characterizing the
covalent and noncovalent interactions between atoms. It is widely accepted that such detailed potentials
are essential to the success of NMA’s. We show that a single-parameter potential is sufficient to
reproduce the slow dynamics in good detail. Costly and inaccurate energy minimizations are eliminated,
permitting direct analysis of crystal coordinates. The technique can be used for new applications, such
as mapping of one crystal form to another by means of slow modes, and studying anomalous dynamics
of large proteins and complexes.
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