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COACH results for job QHD43419

Download the submitted query structure file

COACH Results
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Click to viewRankC-scoreCluster
size
PDB
Hit
Lig
Name
Download
Complex
Consensus Binding Residues
10.11 6 4rku4 G3P Rep, Mult 50,51,54
20.05 3 1z9jB BCL Rep, Mult 46,47
30.04 2 4yu5A KH2 Rep, Mult 93,98,127
40.04 2 3eymB EYK Rep, Mult 47,50,51
50.04 2 2qveA 247 N/A 36,39,42
60.02 1 2pltA CA N/A 165,166
70.02 1 3og2A MAN Rep, Mult 142,195
80.02 1 N/A N/A N/A 78,137,138,139,197,198
90.02 1 N/A N/A N/A 112,114,117,119,132,133,134,170,173,175,177,201
100.02 1 3gjcA BOG N/A 34,37


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.
 
TM-SITE Results
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Click to viewRankC-scoreaCluster
sizeb
Rep
Templc
Mult
Templd
Ligandse Predicted binding site residues
10.29 4 4rku4_BS19_G3P Download HEM(2),G3P(1),DAK(1),.. 50,51,54
20.22 3 3eymB_BS02_EYK Download GTP(1),BCL(1),EYK(1) 47,50,51
30.14 1 2q8hA_BS01_TF4 Download TF4(1) 27,53,88,126,128

(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 0.19 4 List BOG(1),MG(1),295(1),.. 34,36,37,39,42,50
2 0.12 1 List NAP(1) 99,101
3 0.12 1 List MG(1) 153,165
4 0.11 1 List CE1(1) 90,95
5 0.11 1 List CA(1) 18,21

(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
10.013og2A0.416 5.060.0640.6491.00MANDownload11,81
20.013og2A0.416 5.060.0640.6490.57BMADownload96
30.013og2A0.416 5.060.0640.6490.69MANDownload142,195
40.014yu5A0.441 5.580.0600.7160.58KH2Download93,98,127
50.013ogvA0.416 5.080.0640.6490.69NAGDownload45,46,47,49,94

(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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No binding site was predicted by FINDSITE.
 
ConCavity Results
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Click to viewRank C-score Predicted binding residues
1 0.18 34,42,45,97,102,105,107,123
2 0.09 112,114,117,119,132,133,134,170,173,175,177,201
3 0.07 78,137,138,139,197,198





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).