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== Other Useful Resources == | == Other Useful Resources == | ||
- | * [ | + | * [[Macromolecular Geometry]]: Useful programs for structural analysis available for download |
* [http://bioinfo.mbb.yale.edu/geometry/membrane/ Membrane protein motions]: A web page for M Gerstein & C Chothia (1999), "Proteins in Motion" | * [http://bioinfo.mbb.yale.edu/geometry/membrane/ Membrane protein motions]: A web page for M Gerstein & C Chothia (1999), "Proteins in Motion" | ||
* [http://www.molmovdb.org/cocb/ Large scale protein motions]: Gerstein and Echols (2004) | * [http://www.molmovdb.org/cocb/ Large scale protein motions]: Gerstein and Echols (2004) |
Revision as of 22:46, 25 June 2008
MolMovDB and Associated Tools
Contents |
Databases
- Protein motions: Manually curated descriptions of conformational changes in hundreds of distinct proteins, with references and movie links
- 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
- Search database
- 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
- 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 prediction: The new HingeMaster server predicts hinge locations in single protein structures. The algorithm combines FlexOracle, TLSMD, StoneHinge and NSHP hinge predictors for maximum accuracy
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)