COACH-D results for job CH000001 (example)

[Click on CH000001_results.tar.bz2 to download the tarball file including all modeling results listed on this page]

Download the submitted query structure file
Download the submitted query ligand structure

   Predicted ligand-binding sites and poses

Visualization

Top 5 predicitons

Rank Poseu Poset C-score Cluster size PDB template Ligand Downloadu Energyu Downloadt Energyt Predicted binding residues
1 1.00 329 1lwxA AZD Complex -6.2 Complex -5.7 9,50,53,58,62,86,99,106,107,109,111,112
2 0.16 17 3ngsA PO4 Complex -5.0 Complex -2.2 9,50,99,111,112
3 0.14 26 1f3fB PO4 Complex -6.1 Complex -2.4 9,49,50,86,112,113
4 0.12 16 3ngtJ AMP Complex -5.9 Complex -6.1 9,50,53,58,62,106,112
5 0.08 19 3gp9B MG Complex -2.1 Complex -1.4 86,89,99,112,113
Download the detailed prediction summary.
Download the templates clustering results.
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   Summary for ligands in the first-ranked prediciton above

Rank Ligand Frequency PDB template Download

Visualizaiton

1 ADP 51 1b4sA, 1nlkL, 1nlkR, 1ucnA, 1ucnB,
1wklA, 1zs6A, 1zs6B, 1zs6D, 2dy9A,
2hveC, 3nguA, 3nguB, 3q8uA, 3q8uE,
3q8uF, 3q8yA, 3q8yE, 3q8yG, 4dz6A,
SDF file
2 GDP 35 1bhnA, 1bhnB, 1bhnC, 1bhnD, 1bhnE,
1bhnF, 1nueA, 1nueD, 1nueE, 1wkkA,
2dxeA, 3fbeA, 3fbeC, 3fbeF, 3gp9A,
3gp9C, 3gp9D
SDF file
3 CDP 30 2az3A, 2az3B, 2az3F, 2az3G, 2az3H,
2az3I, 3etmA, 3fc9B, 3q89B, 3q89E
SDF file
Others TYD(27), AMP(19), DGI(18), TNM(12), PCG(9), 3AN(9), PPS(7), ANP(6), AZD(6), GTP(6), UDP(6), 35G(6), EOI(4), TBD(3), GNP(3),
D4T(3), ABT(3), TNV(3), ATP(3), CTP(3), CMP(3), DGT(3), FUP(3), DAT(2), DA(2), DG(1),

References

  • Q. Wu, Z. Peng, Y. Zhang, J. Yang, COACH-D: improved protein-ligand binding site prediction with refined ligand-binding poses through molecular docking, Nucleic Acids Research, 46: W438–W442 (2018).
  • J. Yang, A. Roy, Y. Zhang, Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, 29: 2588-2595 (2013).