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COACH results for job QHD43415_9

Download the submitted query structure file

COACH Results

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Click to view	Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Consensus Binding Residues
	1	0.09	4	3p70H	PEPTIDE	Rep, Mult	43,89,90,99,100,103,104
	2	0.05	4	3gukA	CA	Rep, Mult	90,99
	3	0.05	4	4g51C	NO	Rep, Mult	44,102
	4	0.05	4	2xquB	CVM	Rep, Mult	100,103
	5	0.04	2	3rbhD	C8E	Rep, Mult	29,88
	6	0.03	2	4ftsB	Nuc.Acid	Rep, Mult	102,105
	7	0.03	2	2bf6A	CA	N/A	1,2
	8	0.03	2	1k2i1	SN1	Rep, Mult	46,47,48,49,51,72,73,86
	9	0.03	2	4u9kA	NO	Rep, Mult	9,11,102
	10	0.02	1	3EE7D	3EE7D00	Rep, Mult	39,58,59

	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 view	Rank	C-score^a	Cluster size^b	Rep Templ^c	Mult Templ^d	Ligands^e	Predicted binding site residues
	1	0.20	2	2xquB_BS07_CVM	Download	CVM(2)	100,103
	2	0.18	2	4rjkF_BS05_PYR	Download	NUC(1),PYR(1)	105,106
	3	0.17	1	3gukA_BS02_CA	Download	CA(1)	90,99
	4	0.15	1	1pjpA_BS02_ZN	Download	ZN(1)	68,92
	5	0.15	1	3rbhD_BS06_C8E	Download	C8E(1)	29,88

(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-score^a	Cluster size^b	Templates^c	Ligands^d	Predicted binding site residues
	1	0.22	6	List	NUC(3),C10(1),MG(1),..	32,71,73,74,75,92,98,99
	2	0.15	2	List	AHR(1),WO2(1)	3,89,99,100
	3	0.13	1	List	CA(1)	1,2
	4	0.11	1	List	CA(1)	68,70,72

(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 view	Rank	C-score^a	PDB Hit	TM-score	RMSD^b	IDEN^c	Cov^d	BS-score^e	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1qj6B	0.483	3.53	0.077	0.681	0.51	PEPTIDE	Download	9,42,89,91
	2	0.01	4ayvB	0.478	3.67	0.076	0.690	0.54	PEPTIDE	Download	73,75,88,100
	3	0.01	3pmaD	0.477	4.13	0.057	0.743	0.71	SCR	Download	97,100,101,104
	4	0.01	1tb6H	0.477	4.01	0.066	0.735	0.67	GU0	Download	71,72
	5	0.01	1k2i1	0.452	4.21	0.041	0.779	0.52	SN1	Download	46,47,48,49,51,72,73,86

(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 view	Rank	C-score^a	Cluster size^b	Rep Templ^c	Multi Templ^d	Ligands^e	Predicted binding site residues
	1	0.18	2	2J98A00	List	download	11,28,29,31,44,45,46,47,79,84,86,105,106,109,110
	2	0.09	1	3EE7D02	List	download	73,90,99,103
	3	0.09	1	3EE7D01	List	download	13,39
	4	0.09	1	3EE7D00	List	download	38,39,58,59
	5	0.09	1	3EE7C02	List	download	55,57

(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 view	Rank	C-score	Predicted binding residues
	1	0.11	1,3
	2	0.09	45,75,86,103,106,107,110

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).