DAQ-refine is a tool that assesses protein models derived from cryo-EM maps (target resolution: 0-5 A) using the DAQ score and refine the identified regions with errors with modified AlphaFold2.
The output includes a .pdb file documenting the initially scored structure (by DAQ-Score) alongside the refined structure generated by DAQ-Refine.

Our result webpage comprises three tabs: Results Visualization, Output Logs, and Job Configuration.

Results Visualization:
The 'Result Visualization' panel displays both the protein structure before and after refinement by DAQ-Refine.
The B-factor column stores the DAQ(AA) score for each structure.
On the right-hand side, you can click the 'Download Outputs' button to acquire the modeled structure in .pdb format.
The downloaded file includes the original input structure as the 1st model and the refined structure by DAQ-Refine as the 2nd model.
Additionally, you can visualize the map online by clicking the "Show map" button. Once loaded, the default contour level matches your input; however, you can make adjustments by clicking the "..." button beside "isosurface." Within the "Type: Isosurface" option, you can modify the iso-surface value and opacity by scrolling through the bar for precise adjustments. This feature allows you to assess the alignment between the modeled structure and the map.

The 3D models displayed in the panel are color-coded based on the DAQ(AA) score, ranging from red (-1.0) to blue (1.0), employing a 19-residue sliding window. Blue represents a good score, while red signifies a lower score from DAQ.
In MODEL1, the original model depicts all modeled positions colored according to the DAQ(AA) score.
In MODEL2, the DAQ-Refine refined model portrays all modeled positions color-coded based on the DAQ(AA) score.

Output Logs:
The 'Output Logs' panel compiles all outputs generated by the scripts.
If you're interested in monitoring the job's progress during execution, this section provides a comprehensive overview.

Job Configuration:
In the 'Job Configuration' panel, you'll find the input parameters used for this specific job. These records serve to maintain a log of your submitted input for reference.

For any troubleshooting needs: Should you encounter any issues, please don't hesitate to contact us via email to report the problems. When sending an email, kindly use the subject line format 'DAQ-Refine problem: [jobid]', where [jobid] corresponds to the job displayed in the title. This specific identification helps us efficiently locate and debug jobs in the backend, ensuring a prompt response to your concerns.

dkihara@purdue.edu, gterashi@purdue.edu, xiaowang20140001@gmail.com.

DAQ-refine is a protocol using DAQ score to evaluate protein models from cryo-EM maps and employs a modified AlphaFold2 to refine regions with potential errors.

If encounter problems, please contact Daisuke Kihara (dkihara@purdue.edu), Genki Terashi(gterashi@purdue.edu) or Xiao Wang (xiaowang20140001@gmail.com)

Example EMD-2566 chain 9
Input Map file:2566_3J6B_9.mrc

Input protein file:3J6B_9.pdb

Input sequence:3J6B_9 Sequence

Result Example:Result Example

Terashi, G., Wang, X., Kihara, D.. Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score. Acta Cryst. D79 (2022). https://doi.org/10.1107/S2059798322011676
Terashi, G., Wang, X., Maddhuri Venkata Subramaniya, S.R., Kihara, D.. Residue-wise local quality estimation for protein models from cryo-EM maps. Nat Methods 19.9 (2022). https://doi.org/10.1038/s41592-022-01574-4

Please simply click "Schedule Job" when you filled all input fields.

Please see the instruction for How to Preparing the PDB file.

Please see the instruction for How to Preparing the fasta file.

Due to limited computational resources, we can only process proteins with a maximum length of 1500 amino acids for each chain. Also, the processing time can be long, please be patient and wait for the result.

If your turn in a job with the structure >20 chains, it could take one week or more time to finish.

If the chain in the fasta file contains 'X' only, we would not process this chain and delete it in the final result.

Please select the alignment strategy for PDB file and fasta sequence. We strongly recommend you align the 2 files for chains mannually(keep the same order for chains in 2 files), a simple tutorial here. If you are not sure, please select "Smith Waterman alignment".