[Back]

COACH results for job QHD43420

Download the submitted query structure file

COACH Results
Hide

Click to viewRankC-scoreCluster
size
PDB
Hit
Lig
Name
Download
Complex
Consensus Binding Residues
10.12 4 5hk7A VVA Rep, Mult 10,41
20.10 4 1mz9B VDY Rep, Mult 29,33,37
30.08 3 4hchA MG Rep, Mult 41,44
40.08 3 3mnnF MML Rep, Mult 38,42
50.05 2 4tf4A BGC Rep, Mult 5,7,58,59
60.03 1 3g5nA PB2 N/A 20,22,23,25
70.03 1 N/A N/A N/A 12,13,19,22,33,59,61
80.03 1 5a0jA MG Rep, Mult 39,43,46


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
Hide

Click to viewRankC-scoreaCluster
sizeb
Rep
Templc
Mult
Templd
Ligandse Predicted binding site residues
10.27 3 3wmmK_BS05_CRT Download RTL(1),36E(1),VDY(1),.. 29,33,36,44
20.21 2 3u4fA_BS02_MG Download MG(2) 41,44
30.21 2 3mnnF_BS03_MML Download MML(1),CMP(1) 38,42
40.17 1 5hk7A_BS01_VVA Download VVA(1) 10,41
50.17 1 5a0jA_BS03_MG Download MG(1) 39,43,46

(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
Hide

Click to view Rank C-scoreaCluster
sizeb
Templatesc Ligandsd Predicted binding site residues
1 0.30 2 List MG(2) 7,8,11
2 0.19 1 List PB2(1) 20,22,23,25

(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
Hide

Click to viewRankC-scoreaPDB
Hit
TM-scoreRMSDbIDENcCovdBS-scoreeLig. NameDownload
Complex
Predicted binding site residues
10.024tf4A0.504 3.510.1050.8690.65BGCDownload5,7,58,59
20.011dl2A0.500 3.750.0690.9020.52NAGDownload10,13,58
30.013c67A0.494 3.490.0520.8851.10GLCDownload35,38,39,42
40.013w7sB0.496 3.670.0520.9020.70GLCDownload7,41,58
50.011dl2A0.500 3.750.0690.9020.70NAGDownload6,38,40,41

(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
Hide

Click to viewRankC-scoreaCluster
sizeb
Rep
Templc
Multi
Templd
Ligandse Predicted binding site residues
10.05 1 1JQNA00 List download 6,9,52

(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
Hide

Click to viewRank C-score Predicted binding residues
1 0.04 12,13,19,22,33,59,61





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).