Morph3D- 3-D Morphometric software
©Kent Vander Velden
and Gavin Naylor
Iowa State University
Dirac Science Library,
Florida State University,
Tallahassee, FL 32306-4120
- This is a software package
designed to facilitate comparison of protein structures based on 3-D coordinates.
We anticipate that this software will be especially useful for biologists
wishing to understand the relationship between evolutionary change
in sequence and any concommittent change that occurs in structure. As more
data become avaialble it will also be able to investigate whether there
exist trajectories of shape change over evolutionary time.
It is based upon ideas of Geometric
morphometrics originally conceived by Bookstein and Rohlf to compare anatomical
structures. Amino acid sequences are first aligned using a multiple alignment.
This provides the hypothesis for homology (correspondence) among the residues
of different proteins. The 3-D coordinates of each residue are then used
as input data for the program. Structures are translated, rotated
and size standardized to a common reference. The software then conducts
an eigen decomposition of the shape differences between structures as a
series of "partial warps" (based on a bending energy matrix generated from
superimposing one structure onto another)
We have used this feature to estimate
the shapes of ancestral protein structures. We use our understanding of
the phylogenetic relationships among organisms to estimate the points in
the shape space that likely correspond to hat of the common ancestor. We
then look for the particular structure that corresponds to the ancestral
point in the shape space
Click to enlarge
A particularly powerful aspect of the geometric morphometric approach
is the fact that it embodies a reciprocal relationship between a point
in a shape space and a three dimensional representation of a structure.
The user can choose to see what the corresponding structure might look
like at a point in the shape space for which there are no empirical observations.
Comparisons between protein structures generates a high dimensional
shape space within which Procrustes Distance provides a similarity metric
that closely corresponds to a natural sense of overall shape similarity.
Projections from the shape space allow us to visualize shape similarity
as an ordination on a plane.
|3-D morphometry PDB parser:
This feature allows us to aligne the data sequences and the structure
from a PDB file.
A Unix version and Windows version of the software are available.