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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
- Collection of Sets of Motions Database of morphs categorized into distinct sets.
- Protein Packing
- Sets available for batch download: Listing of the motion pairs can be downloaded from here: list.txt.gz
- Help page
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
- Evolmorph Server: A variation of the Morph Server for morphing between conformations of different but related proteins.
- 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.
- RigidFinder: performs comparison of two protein conformations with the aim of identifying movable rigid regions.
- GenoDock: predicts disruptive SNVs for drug ligand-protein binding
Other Useful Resources
- Macromolecular Geometry: Useful programs for structural analysis available for download
- Parts List: A web-based system for dynamic ranking of protein folds based on over 180 disparate attributes.
- 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)
- DynaSIN: Macromolecular motions in the context of protein-protein interaction networks
- Related Resources: Online resources with similar functionality
Publications
- A list of Gerstein lab publications describing applications of the database, or related to protein motions in general
- Samuel Flore's 2005 article in "The Pharma Frontier"
Credits
Uploading your movies
- To upload your movie use the Upload file option under the toolbox menu on the left. Once uploaded you can view your movie under the uploaded movie collection
