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Runs DynDom program on structures for which multiple X-ray crystallographic conformations is available, which relies on identification of rigid domains on the basis of clustered rotation vectorsDynDomLee RA, Razaz M, Hayward S. The DynDom database of protein domain motions. Bioinformatics. 2003 Jul 1;19(10):1290-1.

Database of Simulated Molecular Motions (DSMM)

Built using MySQL, and accessed with PHP, rather than implementing a single algorithm or set of algorithms to generate its own “movies” of macromolecular motions, this database serves as a depository which collects simulations published by other groups from around the worldDSMMFinocchiaro G, Wang T, Hoffmann R, Gonzalez A, Wade RC. DSMM: a Database of Simulated Molecular Motions. Nucleic Acids Res. 2003 Jan 1;31(1):456-7.


More of a visualization tool than an analytical resource, MovieMaker applies Cartesian interpolation in generate graphics on macromolecular movements, and allows the user to specify the type of motion (morphing, folding, docking, etc) and graphics featuresMovieMakerMaiti R, Van Domselaar GH, Wishart DS. MovieMaker: a web server for rapid rendering of protein motions and interactions. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W358-62.


A database which applies normal mode analysis to proteins, using full-atom model representations. Employs dihedral angle space to represent structures, rather than Cartesian coordinatesProModeWako H, Kato M, Endo S. ProMode: a database of normal mode analyses on protein molecules with a full-atom model. Bioinformatics. 2004 Sep 1;20(13):2035-43. Epub 2004 Apr 1.


Applies normal mode analysis to capture the coarse grain representations of motions of large proteins. For most motions, elastic network models are used in performing NMANOMAD-RefLindahl E, Azuara C, Koehl P, Delarue M. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W52-6.
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