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* The [http://www.molmovdb.org/movies/gallery.html highlights] page showcases some of our best movies | * The [http://www.molmovdb.org/movies/gallery.html highlights] page showcases some of our best movies | ||
* [http://molmovdb.org/sets Collection of Sets of Motions] Database of morphs categorized into distinct sets. | * [http://molmovdb.org/sets Collection of Sets of Motions] Database of morphs categorized into distinct sets. | ||
- | * [[Help page]] | + | * [[Protein Packing]] |
+ | * Sets available for batch download: Listing of the motion pairs can be downloaded from here: [[Media:list.txt.gz|list.txt.gz]] | ||
+ | * [[Help page]] | ||
== Servers == | == 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]]: 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]] | * [[Morph Server FAQ]] | ||
- | * [[Evolmorph Server]]: A variation of Morph Server for morphing between conformations of | + | * [[Evolmorph Server]]: A variation of the Morph Server for morphing between conformations of different but related proteins. |
* [http://helix.gersteinlab.org/ Analysis of helix interactions]: Tools for interface analysis of interacting helices and a database of membrane proteins. | * [http://helix.gersteinlab.org/ Analysis of helix interactions]: Tools for interface analysis of interacting helices and a database of membrane proteins. | ||
* [http://molmovdb.org/nma/ 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). | * [http://molmovdb.org/nma/ 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. | * [[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. | * [[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. | ||
+ | * [http://rigidfinder.molmovdb.org/ RigidFinder]: performs comparison of two protein conformations with the aim of identifying movable rigid regions. | ||
+ | * [http://genodock.molmovdb.org/ GenoDock]: predicts disruptive SNVs for drug ligand-protein binding | ||
== Other Useful Resources == | == Other Useful Resources == | ||
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* [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) | ||
* [http://www.molmovdb.org/cosb/ Protein-protein binding motions]: Conformational changes associated with protein-protein interactions; Goh, Milburn and Gerstein (2004) | * [http://www.molmovdb.org/cosb/ Protein-protein binding motions]: Conformational changes associated with protein-protein interactions; Goh, Milburn and Gerstein (2004) | ||
+ | * [http://archive.gersteinlab.org/proj/DynaSIN/ DynaSIN]: Macromolecular motions in the context of protein-protein interaction networks | ||
+ | * [[Related Resources]]: Online resources with similar functionality | ||
== Publications == | == Publications == | ||
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* [http://molmovdb.org/help/PharmaForecast.pdf Samuel Flore's 2005 article in "The Pharma Frontier"] | * [http://molmovdb.org/help/PharmaForecast.pdf Samuel Flore's 2005 article in "The Pharma Frontier"] | ||
== Credits == | == Credits == | ||
- | * [[ | + | * [[Contributors]] |
+ | * [[Citation metrics]] | ||
==Uploading your movies== | ==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 [http://www2.molmovdb.org/wiki/info/index.php/Special:Imagelist uploaded movie collection] | * 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 [http://www2.molmovdb.org/wiki/info/index.php/Special:Imagelist uploaded movie collection] |
Current revision
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