DEMO server for multidomain protein structure assembly

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(The multi-domain protein library was updated on 2022/07/15)

DEMO (Domain Enhanced MOdeling, version 2) is an significantly improved version for automated assembly of full-length structural models of multi-domain proteins by integrating analogous template alignments with deep-learning predicted inter-domain spatial restraints. Starting from individual domain structures, quaternary structure templates that have similar component domains are identified by domain-level structural alignments using TM-align. Meanwhile, inter-domain spatial restraints are predicted by the deep residual neural-network-based predictor DeepPotential. Full-length models are then created by a fast quasi-Newton optimization for rigid-body domain structure assembly, which are guided by the DeepPotential predicted inter-domain restraints, inter-domain distance profiles collected from the top-ranked quaternary templates, and physics-based steric potentials. The final models are selected from the low energy conformations and further refined with fragment-guided molecule dynamics simulations. Large-scaled benchmark tests showed that the performance is significantly beyond its predecessor. (>>more about the server ...)

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DEMO On-line Server [View an example output]

Input the domain structures to be assembled in order:

Input the structure of domain 1 in PDB format (mandatory):
Please copy and paste your structure file here. Sample input

Or upload the stucture file:

Input the structure of domain 2 in PDB format (mandatory):
Please copy and paste your structure file here. Sample input

Or upload the stucture file:

Select this box to input your full-chain sequence (not required but recommended). (Explanation)

Input the full-chain sequence if your domain structures contain overlap, misorder, or discontinuous domain or when you are not sure.
DEMO can automatically deal with these conditions according to the full-chain sequence.
Copy and paste your full sequence below (in FASTA format). Click for an example input:

Or upload the sequence from your local computer:

Email: (not required but recommended, where results will be sent to)

ID: (optional, your given name to this protein)

Option I: Upload template structures to guide the domain assembly.

Option II: Exclude some templates from the template library.

Option III: Upload experimental data to assist the domain assembly.

DEMO Resource:

DEMO News:

2022/04/10: We have updated the program to significantly reduce the processing time.
2021/12/10: DEMO has been updated to DEMO2 by integrating analogous template alignments with deep-learning spatial restraints for high-accuracy domain structure assembly.
2020/12/01: DEMO was used to assemble structures of all multi-domain targets of 'Zhang-Server' which was ranked as the No. 1 protein structure prediction server in the 14th CASP experiment.
2020/01/31: DEMO assembled structures of all multi-domain proteins encoded by the genome of SARS-CoV-2.

References:

Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang. DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research, https://doi.org/10.1093/nar/gkac340, 2022
Xiaogen Zhou, Jun Hu, Chengxin Zhang, Guijun Zhang, Yang Zhang. Assembling multidomain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences, 116: 15930-15938 (2019). [PDF] [Support Information]

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