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EM-SURFER

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A web-based tool for real-time comparison and analysis of Electron Microscopy (EM) density maps. It compares the shape of EM map isosurfaces, generated using author-recommended contour values. Users can either upload an EM map or choose an existing map in the EMDataBank and compare it against maps stored in the EMDataBank. 3D-Zernike Descriptors (3DZD) are utilized for the efficient comparison between EM maps. The web interface will conveniently display a quantitative measure of similarty between the isosurface shape of EM maps, as well as a measure indicating how similar the target isosurface is to the maps retrieved in the search. EM-SURFER provides the users with the option of comparing EM maps using additional contour levels, based on the original values recommended by each map's authors. It also provides filtering features to compare the target only to maps with a similar volume.

Statistics of latest release (Last update: Nov 12, 2017):

All Entries with resolution data 3,180
Entries with resolution <=5Å 291
Entries with resolution >5Å and <=10Å 744
Entries with resolution >10Å and <=15Å 529
Entries with resolution >15Å and <=20Å 540
Entries with resolution >20Å 1,076
 

 

Latest features:

  • Surface representation: Four isosurface representation options are provided. The first one is the isosurface generated at the author-recommended contour level found in the EMDB. Three additional options combine the author-recommended contour level with the isosurface created by increasing the contour value to represent regions of a higher density, which is usually closer to the core of the molecules.

  • User-uploaded maps: EM-SURFER now accepts user EM maps as queries for searches.

  • Volume filter: Enable this filter to compare only against maps with a volume similar to the query map.

  • Batch mode: A batch mode is available to query multiple EM maps, for users who would like to benchmark their methods against our approach.


   
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