Abstract
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. To interpret the structural information contained in EM density maps, alignment of maps is an essential step for structure modeling, comparison of maps, and for database search. Here, we developed VESPER, which captures the similarity of underlying molecular structures embedded in density maps by taking local gradient directions into consideration. Compared to existing methods, VESPER achieved substantially more accurate global and local alignment of maps as well as database retrieval.
Highlights
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy and stored in the public database, Electron Microscopy Data Bank (EMDB)
EM density maps have been rapidly accumulated in the public database, the Electron Microscopy Data Bank (EMDB)[4], which holds over 12,855 entries as of November 2020
The voxel spacing of the maps is set to 7 Å. This vector representation originates from the approach used in MAINMAST, a de novo protein structure modeling method for cryo-electron microscopy (cryo-EM) maps[23,24]
Summary
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. EM-SURFER does not provide a map alignment because it uses rotation-invariant descriptors, and it only performs global matching. Overall, these methods exhibit a limited accuracy in map alignment and a database search, for partial matching. The concept of map alignment has been used in subunit structure fitting to an EM map of a complex structure, where a simulated density of a subunit is generated and fitted Such methods include EMFIT17, FoldHunter[18], ADP_EM19, and SITUS20. We developed a method called VESPER (VEctor-based local SPace ElectRon density map alignment), which performs accurate global and local alignment and comparison of EM maps
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