COACH results for job CH000001 |
Download the 3D structure model
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| Click to view | Rank | C-scorea | Cluster
sizeb | Rep
Templc | Rep
Ligd | Mult
Temple | Consensus Binding Residues |
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1 | 1.00 | 780 | 3dp9A | BIG | Download | 72,98,99,100,172,173,174,192,193,194,195,217,218,228 |
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2 | 0.32 | 90 | 4g89A | SAH | Download | 30,31,72,98,173,193,194,195,214,228 |
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3 | 0.11 | 76 | 1rxsC | PO4 | Download | 30,34,95,96,97,98,195 |
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4 | 0.02 | 12 | 1jysB | ADE | Download | 100,172,173,174,193,194 |
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5 | 0.01 | 10 | 2i4tA | UA2 | N/A | 17,51 |
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6 | 0.01 | 8 | 3df9A | DF9 | Download | 124,127,129,135 |
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7 | 0.00 | 2 | 1I80A | 1I80A01 | Download | 72,173,194,228 |
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8 | 0.00 | 1 | 1nw4F | SO4 | N/A | 34,230,231 |
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9 | 0.00 | 3 | 1rxcF | K | N/A | 52,70,71,72,73,76 |
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10 | 0.00 | 1 | 2HRDB | 2HRDB01 | Download | 176,177,178,179,180,181,182,221 |
| Click here to download the residue-specific binding probability, which is estimated by SVM. |
| Click here to download the predicted bound ligands and detailed prediction summary. |
| Click here to 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 better prediction. |
| (b) | Cluster size is the total number of templates in a cluster. |
| (c) | Rep Templ presents a predicted representative ligand-protein complex structure from a cluster. |
| (d) | Rep Lig is the bound ligand from the template. Click the ligand name to view its information in the BioLiP database. |
| (e) | Mult Templ provides the structures of all ligands in a 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 | 0.58 | 51 | 1rxuF_BS03_THM | Download | ADE(19),ADN(17),URA(15),.. | 72,98,99,100,173,174,175,192,193,194,195,217,218,227 |
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2 | 0.24 | 13 | 3bjeB_BS02_R1P | Download | R1P(8),R2B(3),ADN(2),.. | 30,34,72,95,97,98,173,193,194,195 |
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3 | 0.18 | 8 | 1pr4C_BS01_PO4 | Download | PO4(7),SO4(1) | 29,30,34,95,97,98,195 |
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4 | 0.12 | 1 | 4gljA_BS01_RHB | Download | RHB(1) | 35,71,73,174,194,229,232,233 |
| (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 | 0.47 | 215 | List | URA(21),ADN(17),PO4(15),.. | 30,34,72,95,97,98,99,100,172,173,174,177,179,192,193,194,195,217,218,220 |
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2 | 0.11 | 3 | List | K(3) | 52,70,71,72,73,76 |
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3 | 0.10 | 4 | List | SO4(1),URF(1),MG(1),.. | 107,108,109,217,218,221,223,227,228 |
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4 | 0.10 | 11 | List | ADN(5),R1P(1),UA2(1),.. | 17,51,79 |
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5 | 0.09 | 2 | List | SO4(1),PO4(1) | 31,34,230,231,232 |
| (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 | 0.95 | 4jwtA | 0.888 | 1.41 | 0.963 | 0.915 | 2 | ADE | Download | 99,100,172,173,174,192,193,194,217,218,220,228 |
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2 | 0.80 | 3nm6B | 0.878 | 0.34 | 0.509 | 0.880 | 1.88 | TRS | Download | 30,31,34,98,193,194,195,214,228 |
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3 | 0.59 | 2qtgA | 0.764 | 2.79 | 0.171 | 0.865 | 1.38 | MTH | Download | 31,72,98,99,100,173,192,193,194,195,218 |
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4 | 0.56 | 1ovgA | 0.724 | 3.08 | 0.148 | 0.849 | 1.44 | MDR | Download | 98,99,173,192,193,218,220 |
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5 | 0.55 | 1zl2D | 0.709 | 2.71 | 0.170 | 0.811 | 1.19 | ANU | Download | 98,99,173,174,176,193,194,195,217 |
| (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 | 0.91 | 146 | 1A69A00 | List | download | 31,72,95,98,99,100,170,173,174,175,192,193,194,195,217,218,220,228 |
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2 | 0.01 | 2 | 1RXYA00 | List | download | 120,133,137 |
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3 | 0.01 | 1 | 3O4VB00 | List | download | 71,76,79 |
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4 | 0.01 | 1 | 3O4VA02 | List | download | 136,137,201,205 |
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5 | 0.01 | 1 | 3O4VA01 | List | download | 172,174,177,178,179 |
| (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 | 0.30 | 30,31,34,72,98,99,100,120,170,172,173,174,192,193,194,195,214,218,220,228 |
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2 | 0.13 | 141,142,143,144,200,204,207,208,209,210,212 |
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3 | 0.12 | 74,78,117,118,119,132,134,138,139,141,197,198,201 |
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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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