Results Walkthrough

This is an example of the information a 3DLigandSite results page provides.
You can watch recordings of successful submissions to 3DLigandSite on the help page.
These results were produced for the CASP target T0396. Adjacent to each results section, a description of the information is provided.
If you use 3DLigandSite in any publications, please cite our 2010 paper using the following:

Wass MN, Kelley LA & Sternberg MJ (2010) 3DLigandSite: predicting ligand-binding sites using similar structures. NAR 38 Suppl:W469-73. PubMed

5fc4cfa433ef1 Results

HHSearch Probability Threshold of 80.0% used.

This can be lower than the threshold you set if no results were produced at your threshold.

These results show the top 5 clusters of binding residues that are predicted to interact with ligands. Please click on the black tabs to open or collapse the corresponding data. Submission details contains information about the Job submitted. Sequence View shows binding cluster residues and their location on the protein sequence submitted. A table showing cluster details is shown, and you can use the viewer to select a cluster, where binding residues are highlighted in red.

Submission ID: 60016ef16c19a

Submission Name: 60016ef16c19a

Email Address: None

Protein Sequence:
MLHWGPKYWRSLHLYAIFFSDAPSWKEKYEAIQWILNFIESLPCTRCQHHAFSYLTKNPL
TLNNSEDFQYWTFAFHNNVNNRLNKKIISWSEYKNIYEQSIL

Protein Structure: T0396.pdb

Cluster 1

Cluster 2

Cluster 3

Cluster 4

Cluster 5

Position

Sequence

Cluster 1

Cluster 2

Cluster 3

Cluster 4

Cluster 5

Position

100

104

Sequence

Cluster 1

Cluster 2

Cluster 3

Cluster 4

Cluster 5

Clusters

The clusters are shown below. They are ranked by the number of ligands, the higher the number the more likely the cluster is to be a true cluster. The ligands that bind the cluster can be seen in more detail by hovering over the ligand name, or by clicking on them.

	Number of Ligands	Ligands	Number of Structures
Cluster 1	33	FAD FLAVIN-ADENINE DINUCLEOTIDE : 33	5
Cluster 2	7	CL CHLORIDE ION : 4, SO4 SULFATE ION : 3	2
Cluster 3	4	SO4 SULFATE ION : 3, CL CHLORIDE ION : 1	3
Cluster 4	4	SO4 SULFATE ION : 4	2
Cluster 5	4	SO4 SULFATE ION : 1, CL CHLORIDE ION : 3	2

Binding Information

Click on the cluster tabs to see cluster residues. The probability score is the likelihood of each residue to be involved in binding. On a benchmark set, the average binding residue score is 0.33, and non-binding score is 0.18.

Residue	Amino Acid	Probability (0-1)
3	MET	0.64
4	LEU	0.49
7	GLY	0.63
8	PRO	0.61
10	TYR	0.76
11	TRP	0.81
15	HIS	0.58
40	PHE	0.69
44	LEU	0.6
48	ARG	0.64
49	CYS	0.85
52	HIS	0.21
53	ALA	0.38
74	THR	0.08
75	PHE	0.68
76	ALA	0.52
77	PHE	0.65
78	HIS	0.89
79	ASN	0.8
81	VAL	0.78
82	ASN	0.78
84	ARG	0.6
85	LEU	0.68
87	LYS	0.69
88	LYS	0.12
90	ILE	0.72
95	TYR	0.6
98	ILE	0.78
99	TYR	0.75

Please wait up to 10 seconds for model rendering and residue colouring

Full Structure

Background		ⓘ Select the background colour you want.
Protein		ⓘ Select the colour of the chain of the protein - this will apply it to the chain with DCPs on only.
Ligands		ⓘ Enter the colour to make the ligands.
Representation		ⓘ Change the way atoms are represented in the viewer. .

Binding Residues

Binding		ⓘ Enter the colour to make the residues that are DCPs.
Side-Chains		ⓘ Hide or Show side-chains for binding residues.

ⓘ Hide all ligands and carbohydrates.	ⓘ Show all ligands and carbohydrates.
ⓘ Make the protein model spin.	ⓘ Open the controls menu.
ⓘ Open Fullscreen.	ⓘ Reset Camera

This is your submission identifier.

Download your results here as an archive.

This informs the user which HHSearch Probability is used. If there are no results generated at the threshold the user sets/default (80%), the threshold is reduced by 10% - to a minimum of 60% - until predictions can be made.

Please click these bars to open/close sections of the results. This functionality is disabled here to maintain the descriptions of each section matching the position on the page.

Your submission identifier, submission name, email address, protein sequence of the submission, and the name of the structure file (if uploaded) are shown in this section.

This is an overview of the residues involved in binding in each of the clusters.

This is the colour scheme of clusters identified.

Cluster 1 is the most confident, Cluster 5 the least confident.

Cluster residues are mapped onto a sequence display of residues modelled in the protein structure. There are 60 amino acids displayed per line.

This is where more detailed information about your clusters are displayed.

The 'Clusters' section shows the confidence of each cluster, and the ligands of which they comprise.

The table can be sorted by clicking on the arrows adjacent to the table headers.

Hover over ligands for their full names, or click on them to be taken to the ligand page on the RCSB PDB site.

The total number of ligands and structures in each cluster is provided here, and a Z-score based on these values is used to rank the cluster.

The higher the Z-score, the more confident the cluster.

The 'Binding Information' section shows the residues that bind to ligands in each cluster. The amino acids and a machine learning-based score is generated for each residue which indicates how likely it is to be involved in binding.

Please click on each 'Cluster' button to load the table for the cluster and load the model in the molecular viewer.

Table columns can be sorted by clicking the arrows adjacent to the column headers.

The table is coloured based on the binding score. A deeper blue is indicative of a greater likelihood of binding.

This section contains a molecular viewer which can be used to see the residues and ligands in each cluster on a 3D representation of your protein.

You can change the colours of the structure by adjusting the dropdown boxes on the right-hand side of the viewer, and then clicking 'Apply'.

A number of other buttons are provided here for manipulating the protein structure.

Please note: Extra functionality is available using the Mol* controls (the boxes in the top right of the viewer). This includes showing or hiding ions and changing the representation of the ligands or the protein.

Residue	Amino Acid	Probability (0-1)
28	LYS	0.08
31	TYR	0.36
32	GLU	0.23
35	GLN	0.05

Residue	Amino Acid	Probability (0-1)
25	PRO	0.26
26	SER	0.07
27	TRP	0.25
28	LYS	0.08