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COACH results for job CH000001

Download the 3D structure model

COACH Results
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Click to viewRankC-scoreaCluster
sizeb
Rep
Templc
Rep
Ligd
Mult
Temple
Consensus Binding Residues
11.00 780 3dp9A BIG Download 72,98,99,100,172,173,174,192,193,194,195,217,218,228
20.32 90 4g89A SAH Download 30,31,72,98,173,193,194,195,214,228
30.11 76 1rxsC PO4 Download 30,34,95,96,97,98,195
40.02 12 1jysB ADE Download 100,172,173,174,193,194
50.01 10 2i4tA UA2 N/A 17,51
60.01 8 3df9A DF9 Download 124,127,129,135
70.00 2 1I80A 1I80A01 Download 72,173,194,228
80.00 1 1nw4F SO4 N/A 34,230,231
90.00 3 1rxcF K N/A 52,70,71,72,73,76
100.00 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.
 
TM-SITE Results
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Click to viewRankC-scoreaCluster
sizeb
Rep
Templc
Mult
Templd
Ligandse Predicted binding site residues
10.58 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
20.24 13 3bjeB_BS02_R1P Download R1P(8),R2B(3),ADN(2),.. 30,34,72,95,97,98,173,193,194,195
30.18 8 1pr4C_BS01_PO4 Download PO4(7),SO4(1) 29,30,34,95,97,98,195
40.12 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.
 
S-SITE Results
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Click to view Rank C-scoreaCluster
sizeb
Templatesc Ligandsd Predicted binding site residues
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
2 0.11 3 List K(3) 52,70,71,72,73,76
3 0.10 4 List SO4(1),URF(1),MG(1),.. 107,108,109,217,218,221,223,227,228
4 0.10 11 List ADN(5),R1P(1),UA2(1),.. 17,51,79
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.
 
COFACTOR Results
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Click to viewRankC-scoreaPDB
Hit
TM-scoreRMSDbIDENcCovdBS-scoreeLig. NameDownload
Complex
Predicted binding site residues
10.954jwtA0.888 1.410.9630.9152ADEDownload99,100,172,173,174,192,193,194,217,218,220,228
20.803nm6B0.878 0.340.5090.8801.88TRSDownload30,31,34,98,193,194,195,214,228
30.592qtgA0.764 2.790.1710.8651.38MTHDownload31,72,98,99,100,173,192,193,194,195,218
40.561ovgA0.724 3.080.1480.8491.44MDRDownload98,99,173,192,193,218,220
50.551zl2D0.709 2.710.1700.8111.19ANUDownload98,99,173,174,176,193,194,195,217

(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.
 
FINDSITE Results
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Click to viewRankC-scoreaCluster
sizeb
Rep
Templc
Multi
Templd
Ligandse Predicted binding site residues
10.91 146 1A69A00 List download 31,72,95,98,99,100,170,173,174,175,192,193,194,195,217,218,220,228
20.01 2 1RXYA00 List download 120,133,137
30.01 1 3O4VB00 List download 71,76,79
40.01 1 3O4VA02 List download 136,137,201,205
50.01 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.
 
ConCavity Results
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Click to viewRank C-score Predicted binding residues
1 0.30 30,31,34,72,98,99,100,120,170,172,173,174,192,193,194,195,214,218,220,228
2 0.13 141,142,143,144,200,204,207,208,209,210,212
3 0.12 74,78,117,118,119,132,134,138,139,141,197,198,201





 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).