DiffModeler is a computational tool using a diffusion model to automatically build full protein complex structure from cryo-EM maps at 0-20A resolution.
This is sequence version of DiffModeler, template (from experimental/AlphaFold) will be searched in the backend.
The search is based on blast aginst structure database (AFDB+PDB) to find most similar structures as template for us to model protein complex.
If you only know some of sequences for 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 Sequence:6824.fasta
Contour level: 3.0
Resolution: 5.8
Result Example:Result Example
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 Please use a sequence file with fasta format. Each chain must have a ID line (begin with a carat (">")) and a SEQUENCE line.
For ID line, please only include the chain id without any other information. If multiple chains include the identical sequences, please use comma "," to split different chains.
Example Sequence ID line
>A,B,C,D
MATPAGRRASETERLLTPNPGYGTQVGTSPAPTTPTEEEDLRR
>E,F
VVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQ
which indicates 6 chains with A,B,C,D share the identical sequences and E,F share another identical sequences.
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.
