GPCRmd Workbench

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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 ExAC.

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

Delta-type opioid receptor (4N6H) Go to simulation report

Selection

Structure selection
Quick selection
Show within Å of
Custom selection
Sequence selection
G
36
S
37
P
38
G
39
A
40
R
41
S
42
A
43
S
44
S
45
L
46
A
47
L
48
A
49
I
50
A
51
I
52
T
53
A
54
L
55
Y
56
S
57
A
58
V
59
C
60
A
61
V
62
G
63
L
64
L
65
G
66
N
67
V
68
L
69
V
70
M
71
F
72
G
73
I
74
V
75
R
76
Y
77
T
78
K
79
M
80
K
81
T
82
A
83
T
84
N
85
I
86
Y
87
I
88
F
89
N
90
L
91
A
92
L
93
A
94
D
95
A
96
L
97
A
98
T
99
S
100
T
101
L
102
P
103
F
104
Q
105
S
106
A
107
K
108
Y
109
L
110
M
111
E
112
T
113
W
114
P
115
F
116
G
117
E
118
L
119
L
120
C
121
K
122
A
123
V
124
L
125
S
126
I
127
D
128
Y
129
Y
130
N
131
M
132
F
133
T
134
S
135
I
136
F
137
T
138
L
139
T
140
M
141
M
142
S
143
V
144
D
145
R
146
Y
147
I
148
A
149
V
150
C
151
H
152
P
153
V
154
K
155
A
156
L
157
D
158
F
159
R
160
T
161
P
162
A
163
K
164
A
165
K
166
L
167
I
168
N
169
I
170
C
171
I
172
W
173
V
174
L
175
A
176
S
177
G
178
V
179
G
180
V
181
P
182
I
183
M
184
V
185
M
186
A
187
V
188
T
189
R
190
P
191
R
192
D
193
G
194
A
195
V
196
V
197
C
198
M
199
L
200
Q
201
F
202
P
203
S
204
P
205
S
206
W
207
Y
208
W
209
D
210
T
211
V
212
T
213
K
214
I
215
C
216
V
217
F
218
L
219
F
220
A
221
F
222
V
223
V
224
P
225
I
226
L
227
I
228
I
229
T
230
V
231
C
232
Y
233
G
234
L
235
M
236
L
237
L
238
R
239
L
240
R
241
S
242
V
243
R
244
L
245
L
246
S
247
G
248
S
249
K
250
E
251
K
252
D
253
R
254
S
255
L
256
R
257
R
258
I
259
T
260
R
261
M
262
V
263
L
264
V
265
V
266
V
267
G
268
A
269
F
270
V
271
V
272
C
273
W
274
A
275
P
276
I
277
H
278
I
279
F
280
V
281
I
282
V
283
W
284
T
285
L
286
V
287
D
288
I
289
D
290
R
291
R
292
D
293
P
294
L
295
V
296
V
297
A
298
A
299
L
300
H
301
L
302
C
303
I
304
A
305
L
306
G
307
Y
308
A
309
N
310
S
311
S
312
L
313
N
314
P
315
V
316
L
317
Y
318
A
319
F
320
L
321
D
322
E
323
N
324
F
325
K
326
R
327
C
328
F
329
R
330
Q
331
L
332
C
333
R
334
K
335
P
336
C
337
G
338
GPCR conserved positions

Highly conserved residues and motifs

Most conserved residues

Most conserved residues

Most conserved residues

Most conserved residues

Representation:
Experimental density map
Quick selection
Custom selection
Sequence selection
G
36
S
37
P
38
G
39
A
40
R
41
S
42
A
43
S
44
S
45
L
46
A
47
L
48
A
49
I
50
A
51
I
52
T
53
A
54
L
55
Y
56
S
57
A
58
V
59
C
60
A
61
V
62
G
63
L
64
L
65
G
66
N
67
V
68
L
69
V
70
M
71
F
72
G
73
I
74
V
75
R
76
Y
77
T
78
K
79
M
80
K
81
T
82
A
83
T
84
N
85
I
86
Y
87
I
88
F
89
N
90
L
91
A
92
L
93
A
94
D
95
A
96
L
97
A
98
T
99
S
100
T
101
L
102
P
103
F
104
Q
105
S
106
A
107
K
108
Y
109
L
110
M
111
E
112
T
113
W
114
P
115
F
116
G
117
E
118
L
119
L
120
C
121
K
122
A
123
V
124
L
125
S
126
I
127
D
128
Y
129
Y
130
N
131
M
132
F
133
T
134
S
135
I
136
F
137
T
138
L
139
T
140
M
141
M
142
S
143
V
144
D
145
R
146
Y
147
I
148
A
149
V
150
C
151
H
152
P
153
V
154
K
155
A
156
L
157
D
158
F
159
R
160
T
161
P
162
A
163
K
164
A
165
K
166
L
167
I
168
N
169
I
170
C
171
I
172
W
173
V
174
L
175
A
176
S
177
G
178
V
179
G
180
V
181
P
182
I
183
M
184
V
185
M
186
A
187
V
188
T
189
R
190
P
191
R
192
D
193
G
194
A
195
V
196
V
197
C
198
M
199
L
200
Q
201
F
202
P
203
S
204
P
205
S
206
W
207
Y
208
W
209
D
210
T
211
V
212
T
213
K
214
I
215
C
216
V
217
F
218
L
219
F
220
A
221
F
222
V
223
V
224
P
225
I
226
L
227
I
228
I
229
T
230
V
231
C
232
Y
233
G
234
L
235
M
236
L
237
L
238
R
239
L
240
R
241
S
242
V
243
R
244
L
245
L
246
S
247
G
248
S
249
K
250
E
251
K
252
D
253
R
254
S
255
L
256
R
257
R
258
I
259
T
260
R
261
M
262
V
263
L
264
V
265
V
266
V
267
G
268
A
269
F
270
V
271
V
272
C
273
W
274
A
275
P
276
I
277
H
278
I
279
F
280
V
281
I
282
V
283
W
284
T
285
L
286
V
287
D
288
I
289
D
290
R
291
R
292
D
293
P
294
L
295
V
296
V
297
A
298
A
299
L
300
H
301
L
302
C
303
I
304
A
305
L
306
G
307
Y
308
A
309
N
310
S
311
S
312
L
313
N
314
P
315
V
316
L
317
Y
318
A
319
F
320
L
321
D
322
E
323
N
324
F
325
K
326
R
327
C
328
F
329
R
330
Q
331
L
332
C
333
R
334
K
335
P
336
C
337
G
338
GPCR conserved positions

Highly conserved residues and motifs

Most conserved residues

Most conserved residues

Most conserved residues

Most conserved residues

Selection settings
× Make a selection to display the map.
Apply default representations
2fo-fc fo-fc
Display map
Map color
Pos
Neg
Map style
ISO level
1.5
3
Zoom
0

GPCRmd Toolkit

Interaction network

Hydrogen bonds:

Wernet Nilsson criteria (MDTraj)

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
Include backbone hydrogen bonds
Threshold: %
Ligand receptor contacts
Compute interaction between GPCR and
In trajectory:
Stride:
Threshold:
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
Naltrindole
Water volume distribution
Display map
Map style
Opacity
1
Smoothness
10
ISO level
1
Show Polar residues
Show waters within
Å of protein