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From Info
MolMovDB and Associated Tools
Contents |
Databases
- Protein Motions
- Movies: Thousands of morphs of transitions between PDB files, viewable through a Java applet or as MPEG or GIF movies. Most of these are submissions to the Morph Server by database users
- The highlights page showcases some of our best movies
- Help page
- Collection of Sets of Motions
Servers
- Morph Server: A web-based tool for generating and animating chemically realistic interpolations between two conformations. Now supports RNA, DNA, and multi-subunit complexes.
- Morph Server FAQ
- Analysis of helix interactions: Tools for interface analysis of interacting helices and a database of membrane proteins.
- Normal mode analysis: This tool allows the user to upload a query structure (or choose it from the motions database), calculate its lowest frequency Normal Mode, build the movie of this vibration and compare it with the pre-calculated flexibility regions based on either supplied B-factors or multiple structural alignment for the corresponding fold family (for single-domain queries).
- Hinge Analysis : HingeMaster is a resource for predicting the location of hinges in a protein structure.
- Conformation Explorer : Resource for predicting the holo structure of a protein, and the protein motion, by providing a trajectory of PDB structures connecting the user input structure to the predicted holo structure.
Other Useful Resources
- Macromolecular Geometry: Useful programs for structural analysis available for download
- Membrane protein motions: A web page for M Gerstein & C Chothia (1999), "Proteins in Motion"
- Large scale protein motions: Gerstein and Echols (2004)
- Protein-protein binding motions: Conformational changes associated with protein-protein interactions; Goh, Milburn and Gerstein (2004)
