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EM-Refiner is a Monte Carlo based method for protein structure refinement and determination using Cryo-EM density map. The pipeline consists of three consecutive steps of structure-to-density map superposition, rigid-body fragment adjustments, and atomic-level structure refinement. During the refinement simulations, the backbone structures are kept flexible with movements guided by a composite of physics- and knowledge-based force field, integrated with Cryo-EM density map data. The pipeline is fully automated and suitable for the protein targets with low-to-medium resolution Cryo-EM density map data.

EM-Refiner Online (View an example of EM-Refiner output)

Input initial structural model (File must be in PDB format, click to download example input) (required):

or





Input density map data (File must be in MRC format, click to download example input) (Note and required):







Please input the resolution of density map (e.g. 10 Å) (required):




Email: (required, where results will be sent to.)

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EM-Refiner Download

• EM-Refiner standalone package
• EM-Refiner benchmark dataset collected

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Reference:

• Biao Zhang, Xi Zhang, Robin Pearce, Hongbin Shen, Yang Zhang. A new protocol for atomic-level protein structure modeling and refinement using low-to-medium resolution cryo-EM density maps. Journal of Molecular Biology, 432: 5365-5377 (2020) [PDF] [Support Information]