DynDom3D is a new program for the analysis of domain movements in large, multi-chain, biomolecular complexes. The program is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. Unlike the original DynDom (DynDom1D) the method is blind to atomic bonding and atom type and can therefore be applied to biomolecular complexes containing different constituent molecules such as protein, RNA or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a “rotation space” and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have co-located points. Thus a domain can be identified from the clustering of points from blocks within it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. It has basically five parameters: a minimum domain size (in number of atoms), a ratio of interdomain displacement to intradomain displacement, a grid length, a block factor, and a block occupancy percentage. Details of the program are described in the following paper:

G.Poornam, A. Matsumoto, H. Ishida, S.Hayward, "A method for the analysis of domain movements in large biomolecular complexes", Proteins, 76, p210-212,2009.

Here you can see the results of the application of DynDom3D in Jmol:

1. Hemoglobin
2. Liver alcohol dehydrogenase
3. S-adenosylhomocysteine hydrolase
4. Aspartate transcarbmylase
5. The 70S ribosome (normal mode from an elastic network model)

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