DeepAssembly server

About DeepAssembly

DeepAssembly is designed to automatically construct multi-domain protein or complex structure through inter-domain interactions from deep learning. Starting from the input sequence of multi-domain protein (or protein complex), DeepAssembly first generates MSAs from genetic databases and searches for templates using our in-house PAthreader. Meanwhile, the input sequence is split into single-domain sequences by a domain boundary predictor, and then the structure for each domain is generated by single-domain structure predictor. Subsequently, features extracted from MSAs, templates and domain boundary information are fed into a deep neural network with self-attention to predict rotations, translations between inter-domain residues, and convert them into inter-domain interactions. Finally, DeepAssembly performs the creation of the initial full-length structure using the single-domain structures, followed by multiple steps of iterative population-based rotation angle optimization and atomic-level structure refinements. The domain assembly simulation is driven by the atomic coordinate deviation potential transformed from predicted inter-domain interactions, where the best conformation by our in-house model quality assessment is selected as the final output structure.

Prediction workspace

Choose an assembly workflow

Single chain

Multidomain Protein

Assemble a full-chain structure from domains and predicted inter-domain interactions.

Multiple chains

General Complex

Predict assemblies formed by two or more protein monomers or structures.

Immune complex

Antibody–Antigen

Model antibody–antigen complexes from standardized multi-chain FASTA input.

News

2026/9/19: We have updated DeepAssembly with a specialized structure prediction function for antibody–antigen complexes.
2024/07/13: DeepAssembly version 2.0 (DeepAssembly2) is developed.
2023/05/03: The server adds protein complex structure assembly functioin.
2022/05/28: DeepAssembly was randked No. 1 for the protein structure prediction in the 1 week CAMEO blind test.
2022/05/21: We developed DeepAssembly for multi-domain protein structure assembly.

Reference

Suhui Wang^✝, Jianan Zhuang^✝, Xinyue Cui, Zexin Lv, Dongliang Hou, Guijun Zhang*. High-accuracy structural modeling of antibody-antigen complexes. Communications Biology. DOI: https://doi.org/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: https://doi.org/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: https://doi.org/10.1038/s42003-023-05610-7

Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li*, Guijun Zhang*. Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Communications biology, 6, 243 (2023). DOI: https://doi.org/10.1038/s42003-023-04605-8

Dong Liu^✝, Biao Zhang^✝, Jun Liu, Hui Li*, Le Song*, Guijun Zhang*. Assessing protein model quality based on deep graph coupled networks using protein language model. Briefings in Bioinformatics, 25, bbad420 (2023). DOI: https://doi.org/10.1093/bib/bbad420

DeepAssembly On-line Server [ View multidomain example of output ][ Back to server ]

Input the multidomain protein full-chain sequence in FASTA format (mandatory, Click for an example input).

Or, upload the FASTA file:

Option: Provide your own domain definition.

Input the protein domain 1 in PDB format (mandatory, Click for an example input).

Or, upload the PDB file:

Input the protein domain 2 in PDB format (mandatory, Click for an example input).

Or, upload the PDB file:

Click the "Add model" and "Remove model" buttons below to add or remove structural models.

Option:

Email: (mandatory, where results will be sent to)

Job name: (optional, your given name to this job)

Reference

Suhui Wang^✝, Jianan Zhuang^✝, Xinyue Cui, Zexin Lv, Dongliang Hou, Guijun Zhang*. High-accuracy structural modeling of antibody-antigen complexes. Communications Biology. DOI: https://doi.org/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: https://doi.org/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: https://doi.org/10.1038/s42003-023-05610-7

Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li*, Guijun Zhang*. Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Communications biology, 6, 243 (2023). DOI: https://doi.org/10.1038/s42003-023-04605-8

Dong Liu^✝, Biao Zhang^✝, Jun Liu, Hui Li*, Le Song*, Guijun Zhang*. Assessing protein model quality based on deep graph coupled networks using protein language model. Briefings in Bioinformatics, 25, bbad420 (2023). DOI: https://doi.org/10.1093/bib/bbad420

DeepAssembly On-line Server [ View complex example of output ][ Back to server ]

Input the sequence (in FASTA format) or structure (in PDB format) of the monomer 1 (mandatory, Click for an example input).

Or, upload the FASTA or PDB file:

Input the sequence (in FASTA format) or structure (in PDB format) of the monomer 2 (mandatory, Click for an example input).

Or, upload the FASTA or PDB file:

Option:

Email: (mandatory, where results will be sent to)

Job name: (optional, your given name to this job)

Reference

Suhui Wang^✝, Jianan Zhuang^✝, Xinyue Cui, Zexin Lv, Dongliang Hou, Guijun Zhang*. High-accuracy structural modeling of antibody-antigen complexes. Communications Biology. DOI: https://doi.org/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: https://doi.org/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: https://doi.org/10.1038/s42003-023-05610-7

Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li*, Guijun Zhang*. Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Communications biology, 6, 243 (2023). DOI: https://doi.org/10.1038/s42003-023-04605-8

Dong Liu^✝, Biao Zhang^✝, Jun Liu, Hui Li*, Le Song*, Guijun Zhang*. Assessing protein model quality based on deep graph coupled networks using protein language model. Briefings in Bioinformatics, 25, bbad420 (2023). DOI: https://doi.org/10.1093/bib/bbad420

DeepAssembly On-line Server [ View antibody–antigen example of output ][ Back to server ]

Reference

Suhui Wang^✝, Jianan Zhuang^✝, Xinyue Cui, Zexin Lv, Dongliang Hou, Guijun Zhang*. High-accuracy structural modeling of antibody-antigen complexes. Communications Biology. DOI: https://doi.org/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: https://doi.org/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: https://doi.org/10.1038/s42003-023-05610-7

Kailong Zhao, Yuhao Xia, Fujin Zhang, Xiaogen Zhou, Stan Z. Li*, Guijun Zhang*. Protein structure and folding pathway prediction based on remote homologs recognition using PAthreader. Communications biology, 6, 243 (2023). DOI: https://doi.org/10.1038/s42003-023-04605-8

Dong Liu^✝, Biao Zhang^✝, Jun Liu, Hui Li*, Le Song*, Guijun Zhang*. Assessing protein model quality based on deep graph coupled networks using protein language model. Briefings in Bioinformatics, 25, bbad420 (2023). DOI: https://doi.org/10.1093/bib/bbad420