more Protein structure pdb file and adding disulfide bond

[DENG]

Dear Zhanglab：
Thank you for your online serve！It helps me a lot.
Utilizing your QUARK online prediction server, I found that the structural predictions from your model align more favorably with our mass spectrometry data. Therefore, I am writing to inquire about the possibility of obtaining access to your local version of the model to generate more structural files.
Additionally, I came across a paper that combines disulfide bond prediction with QUARK (DOI: https://doi.org/10.1093/bioinformatics/btv459). I would like to ask if it would be feasible to incorporate disulfide bond constraints as a limiting condition when performing predictions with a local deployment.
Thank you once more for your time.Looking forward to your response.
Best regards.
Xiaoqin DENG

[ITASSERteam]

Dear User,

Thank you for your kind message and for using our QUARK server. We are glad to hear that the predicted structures are helpful for your research.

You can download the standalone package (which includes QUARK) from the C-QUARK download page:
https://zhanggroup.org/C-QUARK/download.html

Please follow the instructions provided in the README file for installation and usage:
https://zhanggroup.org/C-QUARK/download/README.txt

In particular, you may use the parameter “-pipe QE” to perform the original QUARK ab initio simulation.

Regarding your question about incorporating disulfide bond constraints, the current standalone package does not explicitly provide a dedicated option for enforcing such constraints during prediction. However, you may refer to the related literature and documentation for potential customization or modifications.

We hope this will be helpful for your study. Please feel free to contact us if you have any further questions.

Best wishes,
The Yang Zhang Lab
https://zhanggroup.org/