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(a) | C-score is the confidence score of predicted binding site. C-score ranges [0-1], where a higher score indicates a more reliable prediction. |
(b) | Cluster size is the number of templates in a cluster.
| (c) | Rep Templ presents a representaive ligand-protein template from a cluster. The template names are: (PDBIDchain)_(BioLiP site #)_(Ligand ID). Click the corresponding template to download the structure.
| (d) | Mult Templ provides all ligand-protein complex structures in a cluster, where each ligand is separated by "TER".
| (e) | Ligands lists all ligands in a cluster. The numbers in the parentheses are the appearing times of the corresponding ligands. Click the ligand name to visualize its detailed information in BioLiP.
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Click to view | Rank | C-scorea | PDB Hit | TM-score | RMSDb | IDENc | Covd | BS-scoree | Lig. Name | Download Complex | Predicted binding site residues |
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1 | 0.01 | 3dyoC | 0.218 | 9.11 | 0.036 | 0.326 | 0.58 | IPT | Download | 577,578 |
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2 | 0.01 | 1jz8B | 0.223 | 9.15 | 0.051 | 0.335 | 0.71 | LAK | Download | 36,275 |
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3 | 0.01 | 3cmvB | 0.201 | 9.42 | 0.039 | 0.306 | 0.53 | ANP | Download | 294,295,297,298,299,300,312 |
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4 | 0.01 | 3dyoB | 0.223 | 9.20 | 0.051 | 0.335 | 0.95 | IPT | Download | 1002,1006 |
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5 | 0.01 | 3dyoA | 0.223 | 9.17 | 0.053 | 0.336 | 0.72 | IPT | Download | 278,279,280,285,286,287 |
(a) | C-score is the confidence score of predicted binding site. C-score values range in between [0-1]; where a higher score indicates a more reliable prediction. |
(b) | RMSD the RMSD between residues that are structurally aligned by TM-align. |
(c) | IDEN is the percentage sequence identity in the structurally aligned region. |
(d) | 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. |
(e) | 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.
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Click to view | Rank | C-score | Predicted binding residues |
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1 | 0.54 | 303,305,309,310,312,313,662,725,947,950,953,954,957,961,970,999,1002,1003,1006,1010,1014,1021,1028,1041,1042,1044 |
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2 | 0.28 | 740,743,744,745,855,856,966,975,976,978,1000 |
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3 | 0.28 | 828,833,836,847,851,860,956,959,960 |
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4 | 0.23 | 549 |
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Please cite the following articles when you use the COACH server: |
1. | Jianyi Yang, Ambrish Roy and Yang Zhang, Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, 29: 2588-2595 (2013) (download the PDF file) |
2. | Jianyi Yang, Ambrish Roy and Yang Zhang, BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions., Nucleic Acids Research, 41: D1096-D1103 (2013) (download the PDF file). |
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