COACH results for job QHD43415_15 |
Download the submitted query structure file
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| Click to view | Rank | C-score | Cluster
size | PDB
Hit | Lig
Name | Download
Complex | Consensus Binding Residues |
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1 | 0.95 | 67 | 2nyuA | SAM | Rep, Mult | 43,71,72,73,74,79,80,81,99,100,101,113,114,115,130,131,132,170 |
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2 | 0.03 | 5 | 3EVFA | 3EVFA00 | Rep, Mult | 28,29,30,132 |
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3 | 0.03 | 6 | 4n48A | Nuc.Acid | Rep, Mult | 46,74,133,134,170,203 |
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4 | 0.01 | 1 | 4ctjA | 3A9 | Rep, Mult | 50,54,57,60 |
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5 | 0.01 | 1 | N/A | N/A | N/A | 27,29,132,133,172,173,175,202 |
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6 | 0.01 | 2 | 5cuqB | NSC | Rep, Mult | 71,98,99,102,103,114,115,116 |
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7 | 0.01 | 1 | 5cuqA | NSC | Rep, Mult | 71,114,115,116,131 |
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8 | 0.01 | 1 | 2PXCA | 2PXCA02 | Rep, Mult | 40,41,42,43,74,75,76,78 |
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9 | 0.01 | 1 | 3GCZA | 3GCZA01 | Rep, Mult | 138,139,140,141,142,174 |
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10 | 0.01 | 1 | 1av6A | Nuc.Acid | Rep, Mult | 34,45,46,47,49,80,170,203 |
| Download the residue-specific binding probability, which is estimated by SVM. |
| Download the predicted bound ligands and detailed prediction summary. |
| Download the templates clustering results. |
| (a) | C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction. |
| (b) | Cluster size is the total number of templates in a cluster. |
| (c) | Lig Name is the name of possible binding ligand. Click the ligand name to view its information in the BioLiP database. |
| (d) | Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster. |
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| Click to view | Rank | C-scorea | Cluster
sizeb | Rep
Templc | Mult
Templd | Ligandse | Predicted binding site residues |
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1 | 0.50 | 5 | 2nyuA_BS01_SAM | Download | SAM(2),SAH(2),SFG(1) | 43,71,72,73,74,79,80,81,99,100,101,113,114,115,130,131,132,170 |
| (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 | Cluster
sizeb | Templatesc | Ligandsd | Predicted binding site residues |
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1 | 0.51 | 4 | List | SAH(2),SAM(1),SFG(1) | 43,47,71,72,73,74,80,81,99,100,101,114,115,130,131,132,149,170 |
| (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) | Templates presents the list of templates in a cluster. The template names are: (PDBIDchain)_(BioLiP site #)_(Ligand ID). Click the corresponding template to search the BioLiP database. When the number of templates is >5, click "show all templates" to get the list of all templates in the cluster
| | (d) | Ligands lists ligands in a cluster. The numbers in the parentheses are the appearing times for 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 | 0.96 | 2xyvA | 0.954 | 0.30 | 0.944 | 0.956 | 1.99 | SAH | Download | 43,71,72,73,74,80,81,99,100,115,130,131,132,149 |
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2 | 0.09 | 5cuqA | 0.530 | 4.25 | 0.084 | 0.705 | 0.98 | NSC | Download | 71,114,115,116,131 |
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3 | 0.01 | 4n48A | 0.641 | 4.04 | 0.084 | 0.805 | 0.88 | Nuc.Acid | Download | 46,74,133,134,170,203 |
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4 | 0.01 | 4uciA | 0.549 | 3.87 | 0.076 | 0.681 | 0.96 | ADN | Download | 131,132,133,149,170,171 |
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5 | 0.01 | 4ctjA | 0.530 | 4.19 | 0.079 | 0.701 | 0.89 | 3A9 | Download | 50,54,57,60 |
| (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-scorea | Cluster
sizeb | Rep
Templc | Multi
Templd | Ligandse | Predicted binding site residues |
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1 | 0.52 | 17 | 1EIZA00 | List | download | 41,43,46,47,70,71,73,78,79,80,81,99,100,101,114,115,116,130,131,132,133,149,170 |
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2 | 0.15 | 5 | 2E5WA00 | List | download | 25,46,47,78,130,132,133,170,172,199,203 |
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3 | 0.06 | 2 | 2PX8A00 | List | download | 25,26,27,28,29,30,31,134,137,138,143,199,201 |
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4 | 0.06 | 2 | 2HTEA01 | List | download | 29,31,32 |
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5 | 0.03 | 1 | 3GCZA02 | List | download | 27,30,134,137 |
| (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) | 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: (PDBID)(chain)(Ligand #). The ligands have been renamed by FINDSITE as 2-digit numbers. Click the corresponding template to download the structure.
| | (d) | Mult Templ provides the list of all templates in a cluster.
| | (e) | Ligands presents the structures of all ligands in a cluster.
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| Click to view | Rank | C-score | Predicted binding residues |
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1 | 0.46 | 29,30,42,43,46,47,69,71,72,73,74,75,80,81,99,101,130,132,170,172,200,201,203 |
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2 | 0.32 | 27,29,132,133,172,173,175,202 |
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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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