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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

Partially thermostabilized Beta-1 adrenergic receptor in complex with (R)-dobutamine (2Y00.B)
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
A
33
E
34
L
35
L
36
S
37
Q
38
Q
39
W
40
E
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A
42
G
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M
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S
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L
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L
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M
48
A
49
L
50
V
51
V
52
L
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L
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I
55
V
56
A
57
G
58
N
59
V
60
L
61
V
62
I
63
A
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A
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I
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G
67
R
68
T
69
Q
70
R
71
L
72
Q
73
T
74
L
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T
76
N
77
L
78
F
79
I
80
T
81
S
82
L
83
A
84
C
85
A
86
D
87
L
88
V
89
M
90
G
91
L
92
L
93
V
94
V
95
P
96
F
97
G
98
A
99
T
100
L
101
V
102
V
103
R
104
G
105
T
106
W
107
L
108
W
109
G
110
S
111
F
112
L
113
C
114
E
115
C
116
W
117
T
118
S
119
L
120
D
121
V
122
L
123
C
124
V
125
T
126
A
127
S
128
I
129
E
130
T
131
L
132
C
133
V
134
I
135
A
136
I
137
D
138
R
139
Y
140
L
141
A
142
I
143
T
144
S
145
P
146
F
147
R
148
Y
149
Q
150
S
151
L
152
M
153
T
154
R
155
A
156
R
157
A
158
K
159
V
160
I
161
I
162
C
163
T
164
V
165
W
166
A
167
I
168
S
169
A
170
L
171
V
172
S
173
F
174
L
175
P
176
I
177
M
178
M
179
H
180
W
181
W
182
R
183
D
184
E
185
D
186
P
187
Q
188
A
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L
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K
191
C
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Y
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Q
194
D
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P
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G
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C
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C
199
D
200
F
201
V
202
T
203
N
204
R
205
A
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Y
207
A
208
I
209
A
210
S
211
S
212
I
213
I
214
S
215
F
216
Y
217
I
218
P
219
L
220
L
221
I
222
M
223
I
224
F
225
V
226
A
227
L
228
R
229
V
230
Y
231
R
232
E
233
A
234
K
235
E
236
Q
237
I
238
R
239
K
240
I
241
D
242
R
243
A
272
S
273
K
274
R
275
K
276
R
279
V
280
M
281
L
282
M
283
R
284
E
285
H
286
K
287
A
288
L
289
K
290
T
291
L
292
G
293
I
294
I
295
M
296
G
297
V
298
F
299
T
300
L
301
C
302
W
303
L
304
P
305
F
306
F
307
L
308
V
309
N
310
I
311
V
312
N
313
V
314
F
315
N
316
R
317
D
318
L
319
V
320
P
321
D
322
W
323
L
324
F
325
V
326
F
327
F
328
N
329
W
330
L
331
G
332
Y
333
A
334
N
335
S
336
A
337
F
338
N
339
P
340
I
341
I
342
Y
343
C
344
R
345
S
346
P
347
D
348
F
349
R
350
K
351
A
352
F
353
K
354
R
355
L
356
L
357
C
358
GPCR conserved positions

Highly conserved residues and motifs

Most conserved residues

Most conserved residues

Most conserved residues

Most conserved residues

Representation:

GPCRmd Toolkit

Interaction network

Hydrogen bonds:

GetContacts criteria

  • Interacting pairs
  • Inter-helix
  • All
  • Simulation
  • Current frame
  • Summary
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

(R)-DOBUTAMINE

Water distribution
Volume distribution
Display map
Map style
Opacity
0.5
Smoothness
1
ISO level
0.3
Show Polar residues
Show waters within
Å of protein
Dynamic pharmacophores

Display:

Ligand pharmacophores

Receptor pharmacophores

Interaction type:

Color pattern:

Tunnels and channels
Clusters Highest throughput
Style -
c1
c2
c3
c4
c5
c6
c7
c8
c9
c10
c11
c12
c13
c14
c15
Pockets
Show nearby residues?
Smoothing window size:
Pocket number Color Mean volume Avg. Polarity Avg. Hydroph. Density Avg. Hydroph. Score Druggability %

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