Abstract
Protein structure modeling is a fundamental step for the structural interpretation of 3D electron microscopy (EM) density map. Recently, because of the significant progress of the cryo-EM technique, protein structure modeling tools are needed for EM maps determined around 4 Å resolution. At this rear atomic resolution, finding main-chain structure and assigning the amino acid sequence into EM map are still challenging problems. We have developed a de novo modeling tool named MAINMAST for EM maps at near-atomic resolution (~4.5 Å). MAINMAST can trace the backbone structure of a protein from an EM density map directory. We also developed a Graphical User Interface (GUI) plugin of MAINMAST for the UCSF Chimera so that users can monitor structures at each step of a modeling procedure. In this chapter, we demonstrate two examples of the use of MAINMAST software and MAINMAST-GUI to build protein structure model from an EM density map. MAINMAST software and MAINMAST-GUI plugin are freely available for academic users at http://kiharalab.org/mainmast/index.html.
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Acknowledgments
The authors acknowledge C. Christoffer for his help in finalizing the manuscript. This work was partly supported by the National Institutes of Health (R01GM123055), the National Science Foundation (DMS1614777 and CMMI1825941), and the Purdue Institute of Drug Discovery.
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Terashi, G., Zha, Y., Kihara, D. (2020). Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_19
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DOI: https://doi.org/10.1007/978-1-0716-0708-4_19
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