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Summary: Predictions of Protein Flexibility: First-Order Measures
Julio A. Kovacs,1* Pablo Chaco´n,2
and Ruben Abagyan1
1
Department of Molecular Biology, The Scripps Research Institute La Jolla, California
2
Centro de Investigaciones Biolo´gicas (CIB/CSIC) 28040, Madrid, Spain
ABSTRACT The normal modes of a molecule
are utilized, in conjunction with classical conformal
vector field theory, to define a function that mea-
sures the capability of the molecule to deform at
each of its residues. An efficient algorithm is pre-
sented to calculate the local chain deformability
from the set of normal modes of vibration. This is
done by considering each mode as an off-grid sample
of a deformation vector field. Predictions of deform-
ability are compared with experimental data in the
form of dihedral angle differences between two
conformations of ten kinases by using a modified
correlation function. Deformability calculations cor-
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