Morph3D - This is a software package designed to facilitate comparison of protein structures based on 3-D coordinates.

Motivation: 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.

Principle: 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

Demo: Movies  for the two previously described features are available. (1) 3-D Morphometry (Cubes) (2) 3-D Morphometry (Myoglobin) You will probably need one of the following media plug ins (freeware):

Real Player Quick Time Media Player

Features:

Features:	Click to enlarge
2-D morphometry: 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.
3-D morphometry: 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.