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COACH results for job QHD43417

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
10.07 4 2x2vF DPV Rep, Mult 123,126
20.04 2 4cbkL DPV Rep, Mult 115,123,126
30.04 2 3x41A BR Rep, Mult 159,168,170,177
40.04 2 1nuiA ZN N/A 130,133,148,153
50.04 2 2itfC HEM N/A 155,156
60.02 1 4ro2B GLY Rep, Mult 115,118
70.02 1 3v09A UNK Rep, Mult 126,212
80.02 1 1l6mC FE N/A 212,235
90.02 1 N/A N/A N/A 143,144,145,161,162,163,205,208,210,235,237,238,243
100.02 1 2gmrH U10 N/A 220,231


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
10.22 3 2r9rB_BS02_PGW Download DPV(1),PGW(1),RIM(1) 123,127
20.19 2 4cbkL_BS01_DPV Download DPV(1),BCL(1) 115,123,126
30.17 1 3v09A_BS07_UNK Download UNK(1) 126,212
40.17 1 5axsA_BS01_4LF Download 4LF(1) 132,133
50.16 1 2r9rB_BS04_PGW Download PGW(1) 104,105

(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 0.21 5 List ZN(2),HEM(1),MG(1),.. 130,133,148,150,153,155,156,210,221,222
2 0.15 3 List MG(1),FE(1),CA(1) 60,164,183,203,212,235,266
3 0.13 1 List U10(1) 220,231
4 0.12 1 List ZN(1) 182,186

(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
10.013x40B0.442 5.400.0500.6731.08CLDownload159,168,170,176
20.014aw7A0.431 5.520.0210.6620.75L6SDownload101,107,110,111
30.012y8nA0.414 6.380.0460.7090.99SF4Download123,126
40.011rjoA0.440 5.290.0500.6650.88XEDownload158,160,167,169,205

(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 0.18 143,144,145,161,162,163,205,208,210,235,237,238,243
2 0.17 115,118,119,121,122,126,143,212,233,234,244,264,265
3 0.11 10,29,33,35,48,51,52,55,68




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).