DEMO server for multidomain protein structure assembly

Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

(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 ...)

[About] [Download] [Server statistics] [Example output] [Forum]

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]

zhanglab

zhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417