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DEMO Results for job DOT790195786

[Click on DOT790195786_results.tar.bz2 to download the tarball file including all results listed on this page]

Query Sequence and Domain Definition

>example (262 residues)
  • domain 1: 1-94
  • domain 2: 95-262
  • 2 domains in total. Different colors represent different domains.

    Input Individual Domain Structures

    Structure of domain 1 (download dom1.pdb)

    Structure of domain 2 (download dom2.pdb)

    Deep-learning Predicted Distance/Contact Map for Domain Assembly

    CA distance map with distance < 20Å CB distance map with distance < 20Å CA contact map CB contact map
    Download CA distance map
    Download CB distance map
    Download CA contact map
    Download CB contact map

    Top 10 Full-length Templates for Domain Assembly

    Comparison between the best final model and the analogous template

    to view

    (a)Query structure is shown in cartoon, while the structural analogous template is displayed using backbone trace.
    (c)TM-scoreh is the score of the template, which is calculated based on harmonic mean of TM-scores between all domain models and the template.
    (b)Ranking of proteins is based on the TM-scoreh.
    (c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
    (d)IDENb is the percentage sequence identity in the structurally aligned region.
    (e)Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

    Final Full-length Models Assembled by DEMO

    Top 5 models constructed by DEMO

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    eTM-score eRMSD(Å) PDB file
    Model 1 0.95+-0.06 2.5+-1.1 Download model
    Model 2 0.93+-0.07 2.6+-0.9 Download model
    Model 3 0.93+-0.10 2.6+-1.2 Download model
    Model 4 0.90+-0.11 2.8+-0.8 Download model
    Model 5 0.90+-0.13 2.9+-1.0 Download model

    (a)Colored by domain: domain 1 in red; domain 2 in blue.
    (b)For each target, DEMO generates an ensemble of structural conformations by starting from a set of initial models generated by different templates. The server reports up to five final models sorted by the energy. The accuracy of each model is quantitatively evaluated by estimated TM-score (eTM-score) and estimated RMSD (eRMSD) that are calculated based on the significance of the structural analogous templates for domain models assembly, convergence parameters of the domain assembly simulations, satisfaction degrees of the inter-domain distances/interfaces, and the estimated accuracy of the individual domain model. eTM-score is typically in the range of [0,1], where an eTM-score of higher value signifies a model with a high confidence and vice-versa.
    (d)Since the top 5 models are ranked by the energy, it is possible that the lower-rank models have a higher eTM-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests.
    More about eTM-score and eRMSD

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  • Xiaogen Zhou, Chunxiang Peng, Wei Zheng, Yang Li, Guijun Zhang, Yang Zhang. DEMO2: Multi-domain protein structures assembly by coupling quaternary structural alignment with deep-learning inter-domain restraint prediction. Nucleic Acids Research, 50(W1): W235-W245 (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).
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