DiffModeler uses a diffusion model to automatically build full protein complex structures from cryo-EM maps at up to 20 Å resolution.

To use sequences directly, try DiffModeler(seq).

If you only know some chains of the cryo-EM map, you can still run DiffModeler and get good partial structures.

If you encounter problems, please contact Daisuke Kihara (dkihara@purdue.edu) or Han Zhu (zhu773@purdue.edu).

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Example Input

Map File: 6824.mrc
Single-chain PDB files (tar.gz): 6824.tar.gz
Info File: 6824.txt
Contour level: 3.0
Resolution: 5.8

Example Result

View example job

Video Tutorial:

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Please click "Upload" when you have filled in all input fields.

cryo_em_map :

Determine an appropriate contour level for fitting your protein structure. You can also find it interactively on the submission page after uploading your map.

The tool will not work properly without an appropriate contour level.

contour_level :

The map resolution is required as input. If the resolution is 2 Å or better (high resolution), the diffusion step will be skipped.

resolution :

The input file format is updated! You don't need to make a zip file and a config file any more!

Prepare each subunit as a separate PDB file. If you need multiple copies of the same subunit, specify the copy count when uploading.

Both partial subunits and predicted structures (e.g., from AlphaFold) can be used.

To find suitable structures, search the PDB, the AlphaFold Database, or use the EBI Search Tool.

diffmodeler_structure_inputs :

Please select Yes if you want use domain-based structure modeling, the server will use SWORD2 to split each provided chains to domains and model complex based on domains.

domain :
No Yes

Job Note (Optional):
This note will help you distinguish jobs later.