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DMFold results for example2

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Input Sequence In FASTA Format

example2 ( 318 residues )
>protein-A
MKAFTYERVNTPAEAALSAQRVPGAKFIAGGTNLLDLMKLEIETPTHLIDVNGLGLDKIEVTDAGGLRIGALVRNTDLAAHERVRRDYAVLSRALLAGASGQLRNQATTAGNLLQRTRCPYFYDTNQPCNKRLPGSGCAALEGFSRQHAVVGVSEACIATHPSDMAVAMRLLDAVVETITPEGKTRSITLADFYHPPGKTPHIETALLPGELIVAVTLPPPLGGKHIYRKVRDRASYAFALVSVAAIIQPDGSGRVALGGVAHKPWRIEAADAQLSQGAQAVYDTLFASAHPTAENTFKLLLAKRTLASVLAEARAQA

  Multiple Sequence Alignments

Alignment depth: Nf=297.473, number of sequences=6879


  • Download multiple sequence alignment in aln format.
  • Download multiple sequence alignment in a3m format.
    		•

     Predicted Contact And Distance Map

    Contact Map
    		 Distance Map

     Top 5 Final Models From DMFold

    Click
    to view    		 RankDownload PDBpLDDT
    1 model1.pdb.gz 0.98
    2 model2.pdb.gz 0.98
    3 model3.pdb.gz 0.98
    4 model4.pdb.gz 0.98
    5 model5.pdb.gz 0.98

    Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

    (a) DMFold generates a large set of structural models by different MSAs as inputs. These models are ranked by predicted TM-score (pTM-score for multimer) or predicted LDDT (pLDDT for monomer) and top 5 models are selected with the highest predicted scores.

     Residue-level Modeling Quality


    pLDDT of chain A


     Proteins With Similar Structure

    Top 10 structural analogs in PDB (as identified by TM-align)

    Click
    to view    		RankPDB
    Hit    		TM-scoreRMSDaIDENaCov.Download
    Alignment
    15g5gB0.980.811.000.99Download
    25y6qB0.951.500.410.99Download
    31rm6B0.872.230.270.95Download
    41zxiC0.791.850.260.84Download
    51ffuC0.781.970.270.84Download
    67dqxB0.782.060.260.84Download
    71t3qC0.781.980.260.84Download
    83hrdG0.772.440.250.85Download
    94zohB0.762.060.220.82Download
    101wygA0.752.520.160.85Download

    Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

    (a)Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
    (b)Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
    (c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
    (d)IDENa 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.

    Predicted Gene Ontology (GO) Terms


    example2-model1-A/GOsearchresult_final_MF.svg
    Molecular Function (MF)
    GO termCscoreGOName
    GO:00164911.00oxidoreductase activity
    GO:00169030.79oxidoreductase activity, acting on the aldehyde or oxo group of donors
    GO:19013630.77heterocyclic compound binding
    GO:00971590.77organic cyclic compound binding
    GO:00001660.76nucleotide binding
    GO:00506600.75flavin adenine dinucleotide binding

    Download full result of the above consensus prediction.

    Click the graph to show a high resolution version.
    (a)CscoreGO is the confidence score of predicted GO terms. CscoreGO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
    (b)The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by CscoreGO:
    [0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]

    example2-model1-A/GOsearchresult_final_BP.svg
    Biological Process (BP)
    GO termCscoreGOName
    GO:00099871.00cellular process
    GO:00081521.00metabolic process
    GO:00446990.99single-organism process
    GO:00442370.99cellular metabolic process
    GO:00447100.98single-organism metabolic process
    GO:00447630.97single-organism cellular process
    GO:00717040.96organic substance metabolic process
    GO:00442810.96small molecule metabolic process
    GO:19013600.95organic cyclic compound metabolic process
    GO:00464830.95heterocycle metabolic process
    GO:00442380.95primary metabolic process
    GO:00068070.95nitrogen compound metabolic process
    GO:19015640.94organonitrogen compound metabolic process
    GO:00061390.94nucleobase-containing compound metabolic process
    GO:00550860.93nucleobase-containing small molecule metabolic process
    GO:00725210.92purine-containing compound metabolic process
    GO:00442480.92cellular catabolic process
    GO:19015650.90organonitrogen compound catabolic process
    GO:19013610.90organic cyclic compound catabolic process
    GO:00467000.90heterocycle catabolic process
    GO:00447120.90single-organism catabolic process
    GO:00442700.90cellular nitrogen compound catabolic process
    GO:00061440.90purine nucleobase metabolic process
    GO:00725230.89purine-containing compound catabolic process
    GO:00061450.88purine nucleobase catabolic process
    GO:00091150.77xanthine catabolic process
    GO:00551140.56oxidation-reduction process

    Download full result of the above consensus prediction.

    Click the graph to show a high resolution version.
    (a)CscoreGO is the confidence score of predicted GO terms. CscoreGO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
    (b)The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by CscoreGO:
    [0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]

    example2-model1-A/GOsearchresult_final_CC.svg
    Cellular Component (CC)
    GO termCscoreGOName
    GO:00444641.00cell part
    GO:00425970.75periplasmic space
    GO:00160200.51membrane

    Download full result of the above consensus prediction.

    Click the graph to show a high resolution version.
    (a)CscoreGO is the confidence score of predicted GO terms. CscoreGO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.
    (b)The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by CscoreGO:
    [0.4,0.5)[0.5,0.6)[0.6,0.7)[0.7,0.8)[0.8,0.9)[0.9,1.0]


     Predicted Enzyme Commission (EC) Numbers

    Top 5 enzyme homologs in PDB

    Click
    to view    		RankCscoreECPDB
    Hit    		TM-scoreRMSDaIDENaCov.EC NumberPredicted Active Site Residues
    10.0602ckjA0.7282.850.1700.8331.17.1.4 1.17.3.2 NA
    20.0601ikpA0.3467.080.0770.6412.4.2.- NA
    30.0601ojnA0.3936.540.0450.6574.2.2.1 NA
    40.0601i19A0.4875.180.0740.6821.1.3.6 NA
    50.0602e1qA0.7512.570.1750.8461.17.3.2 1.17.1.4 NA

    Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

     Click on the radio buttons to visualize predicted active site residues.
    (a)CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
    (b)TM-score is a measure of global structural similarity between query and template protein.
    (c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
    (d)IDENa is the percentage sequence identity in the structurally aligned region.
    (e)Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

     Predicted Ligand Binding Sites

    Template proteins with similar binding site:

    Click
    to view    		RankCscoreLBPDB
    Hit    		TM-scoreRMSDaIDENaCov.BS-scoreLig. NameDownload
    Complex    		Predicted binding site residues
    1 0.54 1rm6B 0.870 2.23 0.269 0.947 1.37 FAD Download 227,29,30,31,32,33,34,51,75,98,99,107,108,111,112,114,115,163,164,207,212,213,230,237,238,239
    2 0.25 1n5wC 0.790 1.82 0.258 0.840 1.14 FAD Download 332,97,99,103,112,164,230,237,238,239
    3 0.18 1ffv4 0.781 1.97 0.266 0.840 1.32 III Download 11,3,4,6,28,31,32,35,39,40,50,77,100,101,102,105,106,236
    4 0.06 1rm6B 0.870 2.23 0.269 0.947 1.14 SF4 Download 1119,121,122,129,131,138,139,140,157,158,159
    5 0.05 1ffv8 0.781 1.98 0.266 0.840 0.87 III Download 441,233,234,236,239,297,298,301,302,305,309
    6 0.04 2ckjD 0.746 2.66 0.171 0.846 0.83 PO4 Download 1170,243,245,259

    Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

      Click on the radio buttons to visualize predicted binding site and residues.
    (a)CscoreLB is the confidence score of predicted binding site. CscoreLB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
    (b)BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
    (c)TM-score is a measure of global structural similarity between query and template protein.
    (d)RMSDa the RMSD between residues that are structurally aligned by TM-align.
    (e)IDENa is the percentage sequence identity in the structurally aligned region.
    (f)Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

    [Back to server]
    Reference:
  • Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, P Lydia Freddolino, Yang Zhang. Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods, (2024). https://doi.org/10.1038/s41592-023-02130-4.
  • Wei Zheng, Quancheng Liu, Qiqige Wuyun, P. Lydia Freddolino, Yang Zhang. DMFold: A deep learning platform for protein complex structure and function predictions based on DeepMSA2. In preparation.
  • Wei Zheng, Qiqige Wuyun, Peter L Freddolino, Yang Zhang. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. 1-20. Proteins. (2023). doi:10.1002/prot.26585.

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