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bioRxiv · 10.1101/2024.05.16.594509

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

Read, R. J.·Pettersen, E. F.·McCoy, A. J.·Croll, T. I.·Terwilliger, T. C.·Poon, B. K.·Meng, E. C.·Liebschner, D.·Adams, P. D.
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Abstract

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 [A]. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation search step enhances signal-to-noise. A Fourier-space likelihood-based local search approach, based on the previously-published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed. SynopsisLikelihood-based cryo-EM docking using our emplace_local software is faster and more sensitive than our related software, em_placement, when the approximate location of a component is known, and is available conveniently through a plugin to the ChimeraX visualization software.

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Read, R. J., Pettersen, E. F., McCoy, A. J., Croll, T. I., Terwilliger, T. C., Poon, B. K., Meng, E. C., Liebschner, D., Adams, P. D.. 2024-05-16. Likelihood-based interactive local docking into cryo-EM maps in ChimeraX. https://doi.org/10.1101/2024.05.16.594509

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