Input of DeepAssembly server

Text can be pasted into an input box or supplied as a file. The requirements depend on the selected workflow:

01

Multidomain Protein Assembly

Single chain · full-length sequence and domain structures
  • Mandatory: The full-chain amino-acid sequence in FASTA format.
  • Mandatory: Provide protein domain structures in PDB format.
  • Optional: A domain boundary definition. Make sure the full-chain sequence covers the domain structures supplied.
  • Optional: An email address and a job name.
02

Protein Complex Assembly

Multiple chains · one input per monomer
  • Mandatory: The sequence in FASTA format or structure in PDB format for monomer 1 and monomer 2.
  • For each monomer, paste the content in the corresponding box or upload its FASTA or PDB file.
  • Optional: An email address and a job name.
03

Antibody-Antigen Assembly

Immune complex · multi-chain FASTA input
  • Mandatory: Antibody and antigen sequences in a single standard FASTA input, either pasted as text or uploaded as a file.
  • Provide each chain as a separate FASTA entry with a unique sequence identifier. The example FASTA file shows heavy-chain, light-chain, and antigen-chain entries.
  • Optional: An email address and a job name.

Output of DeepAssembly server

After calculation, the job URL opens a results page. The example pages below show the current output layout for each workflow.

Multidomain Protein

The results page displays the input sequence and domain definition, five downloadable assembly models, per-residue lDDT plots, and a compressed results package.

See the example result →

Protein Complex

The results page displays five downloadable complex models with per-residue lDDT plots and a compressed results package.

See the example result →

Antibody-Antigen

The results page displays the input FASTA chains and five downloadable models with scores. The example files also include a score table and a compressed package.

See the example result →

Checking your results

  • After submission, DeepAssembly opens a waiting page at a URL containing your job ID.
  • The waiting page refreshes every five seconds. When calculation finishes, the results page appears at the same URL.
  • If you provide an email address, a link to the results page will be sent to that address when calculation is complete. If you omit the email address, save the waiting-page URL so you can return later.

How to cite DeepAssembly

Please cite the publication relevant to the workflow used in your work:

  • Suhui Wang, Jianan Zhuang, Xinyue Cui, Zexin Lv, Dongliang Hou, Guijun Zhang. High-accuracy structural modeling of antibody-antigen complexes. Communications Biology (2026). DOI: 10.1038/s42003-026-10757-0.
  • Yuhao Xia, Yilin Pu, Suhui Wang, Jianan Zhuang, Dong Liu, Minghua Hou, Guijun Zhang. DeepAssembly2: A web server for protein complex structure assembly based on domain-domain interactions. Journal of Molecular Biology 437, 169128 (2025). DOI: 10.1016/j.jmb.2025.169128.
  • Yuhao Xia, Kailong Zhao, Dong Liu, Xiaogen Zhou, Guijun Zhang. Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning. Communications Biology 6, 1221 (2023). DOI: 10.1038/s42003-023-05610-7.