Nucleic Acids Research, Vol 26, Issue 18 4280-4290, Copyright © 1998 by Oxford University Press
M Gerstein and W Krebs
We describe a database of macromolecular motions meant to be of general use
to the structural community. The database, which is accessible on the World
Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB ,
attempts to systematize all instances of protein and nucleic acid movement
for which there is at least some structural information. At present it
contains >120 motions, most of which are of proteins. Protein motions
are further classified hierarchically into a limited number of categories,
first on the basis of size (distinguishing between fragment, domain and
subunit motions) and then on the basis of packing. Our packing
classification divides motions into various categories (shear, hinge,
other) depending on whether or not they involve sliding over a continuously
maintained and tightly packed interface. In addition, the database provides
some indication about the evidence behind each motion (i.e. the type of
experimental information or whether the motion is inferred based on
structural similarity) and attempts to describe many aspects of a motion in
terms of a standardized nomenclature (e.g. the maximum rotation, the
residue selection of a fixed core, etc.). Currently, we use a standard
relational design to implement the database. However, the complexity and
heterogeneity of the information kept in the database makes it an ideal
application for an object-relational approach, and we are moving it in this
direction. Specifically, in terms of storing complex information, the
database contains plausible representations for motion pathways, derived
from restrained 3D interpolation between known endpoint conformations.
These pathways can be viewed in a variety of movie formats, and the
database is associated with a server that can automatically generate these
movies from submitted coordinates.
ARTICLES
A database of macromolecular motions
Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA. mark.gerstein@yale.edu
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