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GPCRmd Workbench

How to use it

Indicate what you want to display in your molecular representation using the selection options of the GPCRmd Viewer.

You can choose one of the selections we propose or define a new one (Customized selection option) using the NGL selection language.

Protein residues can be indicated as generic GPCR residue numbers (Ballesteros-Weinstein or GPCRdb structure-based numbering).

Visualization and trajectory sharing powered by NGL Viewer and MDsrv.

The hydrogen bonding network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

Mutant and variant information obtained from GPCRdb and gnomAD.

Mouse controls:

Left button hold and move: rotate camera around center.

Left button click: pick atom or distance.

Middle button hold and move: zoom camera in and out.

Middle button click: center camera on atom.

Right button hold and move: translate camera in screen plane.

For more information, see the docs.

GPCRmd Viewer

Type-1 angiotensin II receptor with olmesartan (4ZUD.A)
Simulation report and files

Selection

Structure selection
Quick selection
Show within Å of
Custom selection

Input your selection using the NGL selection language. Generic GPCR residue numbering can also be used (more info here).

Sequence selection
K
12
R
13
I
14
Q
15
D
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D
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C
18
P
19
K
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A
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G
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R
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H
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N
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Y
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I
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F
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V
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M
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I
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P
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T
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L
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Y
35
S
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I
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G
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N
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V
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I
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Y
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F
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Y
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M
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K
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K
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T
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V
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A
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S
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V
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F
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L
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L
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N
69
L
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A
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L
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A
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D
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L
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C
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F
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L
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L
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T
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L
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P
82
L
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W
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A
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V
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Y
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T
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A
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M
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E
91
Y
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R
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W
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P
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F
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G
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N
98
Y
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L
100
C
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K
102
I
103
A
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S
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A
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S
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V
108
S
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F
110
N
111
L
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Y
113
A
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S
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V
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F
117
L
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L
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T
120
C
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L
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S
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I
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D
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R
126
Y
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L
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A
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I
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V
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H
132
P
133
M
134
K
135
S
136
R
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L
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R
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R
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T
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M
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L
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V
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A
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K
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T
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C
149
I
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I
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I
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W
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L
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A
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G
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A
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S
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I
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H
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N
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E
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N
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N
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T
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C
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F
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H
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Y
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E
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Q
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N
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P
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G
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L
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T
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K
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N
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L
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G
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L
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F
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P
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F
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L
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I
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I
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L
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T
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S
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Y
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T
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L
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W
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K
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A
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L
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K
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K
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Y
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E
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Q
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N
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K
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N
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D
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D
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F
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K
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I
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M
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A
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V
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F
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F
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F
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P
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H
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Q
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T
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D
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Q
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G
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D
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T
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M
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T
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I
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C
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I
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A
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Y
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F
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N
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N
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C
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L
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N
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P
299
L
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F
301
Y
302
G
303
F
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L
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G
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K
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K
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F
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K
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R
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Y
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F
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L
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Q
315
L
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L
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K
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Y
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I
320
GPCR conserved positions

Highly conserved residues and motifs

Most conserved residues

Most conserved residues

Most conserved residues

Most conserved residues

Representation:

GPCRmd Toolkit

Interaction frequencies
Hydrogen bonds

Trajectory:

Frames:

All

From to

Selection:

Do not include hydrogen bonds between neighbours

All hydrogen bonds

Only side chain hydrogen bonds

Threshold: %
Ligand receptor contacts

Compute interaction between GPCR and

In trajectory:

Stride:

Threshold: Å

Consider

Salt bridges

Trajectory:

Frames:

All

From to

Threshold: %

Distance

Select distances from the viewer by clicking on the atoms. Afterwards, import your selections by clicking at the import button (). You can also manually introduce the atom indices.

Compute distance between and

In trajectory:

Stride:

RMSD

Trajectory:

Frames:

All

From to

Stride:

Reference: frame from trajectory

Selection:

Protein alpha carbons

Protein CA, CB, C, N, O

Non-hydrogen protein atoms

All protein atoms

Olmesartan

Breathing motions

We classify GPCR breathing motions in a simulation "open", "intermediate" or "closed". This classification is based on a specific distance between TM2 and TM6, plotted bellow.

Plot breathing distance by

Download trajectory clustered by conformations:

Filtering trajectory frames. Please be patient, this might take a few minutes....
Genetic variants
Display
Color by:
Show every atom:
Top disease label:
Filter by aminoacid change:
Filter by functional site:
Filter by predicted impact:
Download
Allosteric Paths (AP)

Number of paths

Specify path

Download AP data

Results

Show selected only
Clear selection

0

1

0

-1
An unexpected error occurred.
No AP values are avaliable yet for this parameters selection.

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