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== Databases ==
== Databases ==
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* [http://www.molmovdb.org/cgi-bin/browse.cgi Protein motions]: Manually curated descriptions of conformational changes in hundreds of distinct proteins, with references and movie links
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*[[Protein Motions]]
* [http://molmovdb.org/cgi-bin/movie.cgi 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
* [http://molmovdb.org/cgi-bin/movie.cgi 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
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* [http://www2.molmovdb.org/cgi-bin/search.cgi Search database]
 
* 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
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* [http://molmovdb.org/sets Collection of Sets of Motions] Database of morphs categorized into distinct sets.
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* [[Protein Packing]]
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* Sets available for batch download: Listing of the motion pairs can be downloaded from here: [[Media:list.txt.gz|list.txt.gz]]
* [[Help page]]
* [[Help page]]
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* [http://molmovdb.org/sets Collection of Sets of Motions]
 
== Servers ==
== Servers ==
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* [[Morph Server]]: A web-based tool for generating and animating chemically realistic interpolations between two conformations. Now supports RNA, DNA, and multi-subunit complexes
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* [[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]]
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* [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)
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* [[Evolmorph Server]]: A variation of the Morph Server for morphing between conformations of different but related proteins.
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* [[Hinge Analysis]]
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* [http://helix.gersteinlab.org/ Analysis of helix interactions]: Tools for interface analysis of interacting helices and a database of membrane proteins.
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* [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).
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* [[Hinge Analysis]] : HingeMaster is a resource for predicting the location of hinges in a protein structure.
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* [[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.
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* [http://rigidfinder.molmovdb.org/ RigidFinder]: performs comparison of two protein conformations with the aim of identifying movable rigid regions.
== Other Useful Resources ==
== Other Useful Resources ==
* [[Macromolecular Geometry]]: Useful programs for structural analysis available for download
* [[Macromolecular Geometry]]: Useful programs for structural analysis available for download
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* [http://bioinfo.mbb.yale.edu/align/ Parts List]: A web-based system for dynamic ranking of protein folds based on over 180 disparate attributes.
* [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)
* [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)
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* [http://archive.gersteinlab.org/proj/DynaSIN/ DynaSIN]: Macromolecular motions in the context of protein-protein interaction networks
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* [[Related Resources]]: Online resources with similar functionality
== Publications ==
== Publications ==
* [http://papers.gersteinlab.org/papers/subject/motions/ A list of Gerstein lab publications describing applications of the database, or related to protein motions in general]
* [http://papers.gersteinlab.org/papers/subject/motions/ A list of Gerstein lab publications describing applications of the database, or related to protein motions in general]
* [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"]
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== Credits ==
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* [[Contributors]]
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* [[Citation metrics]]
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==Uploading your movies==
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* 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]

Revision as of 03:24, 3 January 2012

MolMovDB and Associated Tools

Contents

Databases

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.

Other Useful Resources

Publications

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
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