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COACH results for job QHD43415_12

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	0.30	20	4c30F	ANP	Rep, Mult	261,262,283,284,285,286,287,288,289,290,404,442,443,540,567
	2	0.14	7	2gk6A	PO4	Rep, Mult	284,285,288,404,443,538,567
	3	0.13	8	5eawA	ADP	Rep, Mult	261,262,287,288,289,290,320,442
	4	0.02	2	4n0oA	Nuc.Acid	Rep, Mult	181,309,310,311,359,361,362,378,407,408,515,516,532,534,535,560
	5	0.02	2	2gjkA	MG	N/A	289,375,538
	6	0.01	1	2xzlA	ZN	N/A	50,55,72,84
	7	0.01	1	2IS1E	2IS1E00	Rep, Mult	288,538,540
	8	0.01	1	2IS6C	2IS6C01	Rep, Mult	538,539,540,541
	9	0.01	1	3GPLA	3GPLA00	Rep, Mult	177,178,179,180,181,197,214,309,310,311,334,335,336,337,338,339,408,409,410,411,412,413,414,485,486,516,534,554,560
	10	0.01	1	N/A	N/A	N/A	178,284,285,287,288,289,309,310,320,375,378,404,405,406,408,443,513,514,515,516,532,534,537,538,540,554,557,559,560,567

	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	0.31	2	2gk6A_BS02_PO4	Download	CA(1),PO4(1)	284,285,288,404,443,538,567
	2	0.26	2	4n0oA_BS01_NUC	Download	NUC(2)	181,309,310,311,359,361,362,378,407,408,515,516,532,534,535,560

(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	0.20	3	List	UUU(2),ANP(1)	254,255,257,260,284,285,286,287,288,289,290,320,404,442,443,538,540,567
	2	0.18	2	List	MG(2)	289,375,538
	3	0.14	1	List	PO4(1)	284,285,288,404,443,538,567
	4	0.07	1	List	ZN(1)	50,55,72,84
	5	0.07	1	List	ZN(1)	16,19,33,39

(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	0.48	2gk6A	0.675	3.73	0.184	0.770	1.00	ADP	Download	287,288,289,290,320,442
	2	0.30	2gk6A	0.675	3.73	0.184	0.770	1.39	PO4	Download	284,285,288,404,443,538,567
	3	0.05	4n0oC	0.541	4.66	0.155	0.652	1.30	CA	Download	284,288,404,567

(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	0.80	8	1QHGA00	List	download	263,265,284,285,286,287,288,289,290,320,375,404,442,443,537,538,540,567
	2	0.10	1	3GPLA00	List	download	118,310,311,332,336,337,338,408,515,516,532,534,535,554,555
	3	0.10	1	2IS6C01	List	download	312,539,541

(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	0.66	178,284,285,287,288,289,309,310,320,375,378,404,405,406,408,443,513,514,515,516,532,534,537,538,540,554,557,559,560,567

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).