StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement
| العنوان: | StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement |
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| المؤلفون: | Wolfgang Lugmayr, Vadim Kotov, Nikolaus Goessweiner-Mohr, Jiri Wald, Frank DiMaio, Thomas C. Marlovits |
| المصدر: | Nature Protocols. 18:239-264 |
| بيانات النشر: | Springer Science and Business Media LLC, 2022. |
| سنة النشر: | 2022 |
| مصطلحات موضوعية: | General Biochemistry, Genetics and Molecular Biology |
| الوصف: | Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires significant hands-on experience and manual intervention. We recently developed StarMap, an easy-to-use interface between the popular structural display program ChimeraX and Rosetta, a powerful molecular modeling engine. StarMap offers a general approach for refining structural models of biological macromolecules into cryo-EM density maps by combining Monte Carlo sampling with local density-guided optimization, Rosetta-based all-atom refinement and real-space B-factor calculations in a straightforward workflow. StarMap includes options for structural symmetry, local refinements and independent model validation. The overall quality of the refinement and the structure resolution is then assessed via analytical outputs, such as magnification calibration (pixel size calibration) and Fourier shell correlations. Z-scores reported by StarMap provide an easily interpretable indicator of the goodness of fit for each residue and can be plotted to evaluate structural models and improve local residue refinements, as well as to identify flexible regions and potentially functional sites in large macromolecular complexes. The protocol requires general computer skills, without the need for coding expertise, because most parts of the workflow can be operated by clicking tabs within the ChimeraX graphical user interface. Time requirements for the model refinement depend on the size and quality of the input data; however, this step can typically be completed within 1 d. The analytical parts of the workflow are completed within minutes. |
| تدمد: | 1750-2799 1754-2189 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e0cc55be6a2f04018e9b3d9fa7287a8c https://doi.org/10.1038/s41596-022-00757-9 |
| حقوق: | CLOSED |
| رقم الأكسشن: | edsair.doi.dedup.....e0cc55be6a2f04018e9b3d9fa7287a8c |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 17502799 17542189 |
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