DiffModeler is a computational tool using a diffusion model to automatically build full protein complex structure from cryo-EM maps at 0-20A resolution.
If you want to directly use sequence to search rcsb+afdb template, please use DiffModeler sequence version DiffModeler(seq).
If you only know some chains of the cryo-EM map, you can also run DiffModeler and get good partial structures.
If encounter problems, please contact Daisuke Kihara (dkihara@purdue.edu), Xiao Wang (xiaowang20140001@gmail.com) or Han Zhu (zhu773@purdue.edu).
Example EMD-6824 Input Map file:6824.mrc
Input Zip file (including all AlphaFold/Template single-chain pdb files):6824.tar.gz
Input Info file:6824.txt
Contour level: 3.0
Resolution: 5.8
Result Example:Result Example
Video Tutorial:
Please simply click "Schedule Job" when you filled all input fields.
Contour level for input map, suggested [author_contour]. If [author_contour] can not cover structure well, please use contour based on your expertise.
Please make sure your contour level is lower than your focused region. This is absolute density threshold, not standard deviation.
Please do not input 0, you must provide a contour to remove the outside very noisy regions.
For 0-2A resolution, the diffusion process will be skipped. Therefore, if you want to use diffusion model, please just use an approximate resolution of your map.
Please zip all single-chain pdb files to a .zip/.tar.gz/.tar file to upload. We can also model part of protein complex if you only know partial single-chain structure.
Please check AlphaFold Database for single-chain structure with UniProt ID.
You can also search EBI Search Tool aginst structure database to find most similar structures as template for us to model protein complex.
pdb_config_file is a text file (only .txt file accepted) where each line includes pdb file name in the zipped file and its corressponding chains. It can correspond to many identical chains.
Example config file
Suppose you have p142.pdb (corresponds to A, B chain) and p143.pdb (corresponds C chain) in the zip files, then the config file should be
p142.pdb A B
p143.pdb C
Each line of the config file should be "[file_name] [chain_id1]". If one template corresponds to multiple chains, please simply add the chain id in the same line and split by the blank space.
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.
