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Fit to serve

SBKB [doi:10.1038/sbkb.2011.43]
Technical Highlight - October 2011
Short description: A new web server promises to make MultiFit even more accessible and easy to use.

A model of GroEL generated using MultiFit. Reprinted with permission from Nucleic Acid Res 1 .

Electron microcopy (EM) is one of the most powerful and widely used tools to assess the structure of multisubunit proteins and protein complexes. For lower-resolution EM data, an essential second step is to fit atomic-level structures of proteins into the EM density maps, allowing researchers to map out relevant molecular interactions. Already, there are several algorithms available to assist with this process, each with their own strengths.

One such algorithm is MultiFit, a module in the Integrative Modeling Platform that relies on geometric and quality-of-fit criteria to dock protein structures into EM density maps. Now, Sali, Wolfson and colleagues have developed a web interface for MultiFit that greatly increases its accessibility and ease of use. Through the interface, researchers upload their EM density maps (minimum resolution 25 Å) and protein structure data (PDB format), then input relevant parameters and specify how they would like to receive results (link via email or bookmarked link). The MultiFit Webserver can handle both symmetrical and nonsymmetrical EM structures; in the case of the latter, researchers need to input the number of copies of each subunit. For the former, the degree of symmetry is needed.

MultiFit then produces the 20 best models, which can be downloaded as PDB files, UCSF Chimera files or a single compressed file of all models for further analysis. A run on the server usually takes approximately 20 min and includes an output file that lists a quality-of-fit score for each model. With MultiFit taking such a short amount of time and the results so easily assessed, this new, free server is likely to see a lot of traffic as an ever-increasing number of multisubunit complexes is analyzed by EM.

Steve Mason

References

  1. E. Tjioe & K. Lasker et al. MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.
    Nucleic Acids Res. 39, W167-W170 (2011). doi:10.1093/nar/gkr490

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