Free cookie consent management tool by TermsFeed GPCRmd
× Due to a recent server update, this page will be slow for the next 1-2 hours. We apologize for any inconvenience this may cause.

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

Adenosine receptor A2a in complex with xanthine amine congener (3REY.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
P
2
I
3
M
4
G
5
S
6
S
7
V
8
Y
9
I
10
T
11
V
12
E
13
L
14
A
15
I
16
A
17
V
18
L
19
A
20
I
21
L
22
G
23
N
24
V
25
L
26
V
27
C
28
W
29
A
30
V
31
W
32
L
33
N
34
S
35
N
36
L
37
Q
38
N
39
V
40
T
41
N
42
Y
43
F
44
V
45
V
46
S
47
L
48
A
49
A
50
A
51
D
52
I
53
A
54
V
55
G
56
V
57
L
58
A
59
I
60
P
61
F
62
A
63
I
64
T
65
I
66
S
67
T
68
G
69
F
70
C
71
A
72
A
73
C
74
H
75
G
76
C
77
L
78
F
79
I
80
A
81
C
82
F
83
V
84
L
85
V
86
L
87
T
88
Q
89
S
90
S
91
I
92
F
93
S
94
L
95
L
96
A
97
I
98
A
99
I
100
D
101
R
102
Y
103
I
104
A
105
I
106
R
107
I
108
P
109
L
110
R
111
Y
112
N
113
G
114
L
115
V
116
T
117
G
118
T
119
R
120
A
121
K
122
G
123
I
124
I
125
A
126
I
127
C
128
W
129
V
130
L
131
S
132
F
133
A
134
I
135
G
136
L
137
T
138
P
139
M
140
L
141
G
142
W
143
N
144
N
145
C
146
G
147
Q
148
P
149
K
150
E
151
G
152
K
153
N
154
H
155
S
156
Q
157
G
158
C
159
G
160
E
161
G
162
Q
163
V
164
A
165
C
166
L
167
F
168
E
169
D
170
V
171
V
172
P
173
M
174
N
175
Y
176
M
177
V
178
Y
179
F
180
N
181
F
182
F
183
A
184
C
185
V
186
L
187
V
188
P
189
L
190
L
191
L
192
M
193
L
194
G
195
V
196
Y
197
L
198
R
199
I
200
F
201
L
202
A
203
A
204
R
205
R
206
Q
207
L
208
K
209
Q
210
M
211
E
212
S
213
Q
214
P
215
L
216
P
217
G
218
E
219
R
220
A
221
R
222
S
223
T
224
L
225
Q
226
K
227
E
228
V
229
H
230
A
231
A
232
K
233
S
234
L
235
A
236
I
237
I
238
V
239
G
240
L
241
F
242
A
243
L
244
C
245
W
246
L
247
P
248
L
249
H
250
I
251
I
252
N
253
C
254
F
255
T
256
F
257
F
258
C
259
P
260
D
261
C
262
S
263
H
264
A
265
P
266
L
267
W
268
L
269
M
270
Y
271
L
272
A
273
I
274
V
275
L
276
S
277
H
278
T
279
N
280
S
281
V
282
V
283
N
284
P
285
F
286
I
287
Y
288
A
289
Y
290
R
291
I
292
R
293
E
294
F
295
R
296
Q
297
T
298
F
299
R
300
K
301
I
302
I
303
R
304
S
305
H
306
V
307
L
308
R
309
Q
310
Q
311
E
312
P
313
F
314
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
P
2
I
3
M
4
G
5
S
6
S
7
V
8
Y
9
I
10
T
11
V
12
E
13
L
14
A
15
I
16
A
17
V
18
L
19
A
20
I
21
L
22
G
23
N
24
V
25
L
26
V
27
C
28
W
29
A
30
V
31
W
32
L
33
N
34
S
35
N
36
L
37
Q
38
N
39
V
40
T
41
N
42
Y
43
F
44
V
45
V
46
S
47
L
48
A
49
A
50
A
51
D
52
I
53
A
54
V
55
G
56
V
57
L
58
A
59
I
60
P
61
F
62
A
63
I
64
T
65
I
66
S
67
T
68
G
69
F
70
C
71
A
72
A
73
C
74
H
75
G
76
C
77
L
78
F
79
I
80
A
81
C
82
F
83
V
84
L
85
V
86
L
87
T
88
Q
89
S
90
S
91
I
92
F
93
S
94
L
95
L
96
A
97
I
98
A
99
I
100
D
101
R
102
Y
103
I
104
A
105
I
106
R
107
I
108
P
109
L
110
R
111
Y
112
N
113
G
114
L
115
V
116
T
117
G
118
T
119
R
120
A
121
K
122
G
123
I
124
I
125
A
126
I
127
C
128
W
129
V
130
L
131
S
132
F
133
A
134
I
135
G
136
L
137
T
138
P
139
M
140
L
141
G
142
W
143
N
144
N
145
C
146
G
147
Q
148
P
149
K
150
E
151
G
152
K
153
N
154
H
155
S
156
Q
157
G
158
C
159
G
160
E
161
G
162
Q
163
V
164
A
165
C
166
L
167
F
168
E
169
D
170
V
171
V
172
P
173
M
174
N
175
Y
176
M
177
V
178
Y
179
F
180
N
181
F
182
F
183
A
184
C
185
V
186
L
187
V
188
P
189
L
190
L
191
L
192
M
193
L
194
G
195
V
196
Y
197
L
198
R
199
I
200
F
201
L
202
A
203
A
204
R
205
R
206
Q
207
L
208
K
209
Q
210
M
211
E
212
S
213
Q
214
P
215
L
216
P
217
G
218
E
219
R
220
A
221
R
222
S
223
T
224
L
225
Q
226
K
227
E
228
V
229
H
230
A
231
A
232
K
233
S
234
L
235
A
236
I
237
I
238
V
239
G
240
L
241
F
242
A
243
L
244
C
245
W
246
L
247
P
248
L
249
H
250
I
251
I
252
N
253
C
254
F
255
T
256
F
257
F
258
C
259
P
260
D
261
C
262
S
263
H
264
A
265
P
266
L
267
W
268
L
269
M
270
Y
271
L
272
A
273
I
274
V
275
L
276
S
277
H
278
T
279
N
280
S
281
V
282
V
283
N
284
P
285
F
286
I
287
Y
288
A
289
Y
290
R
291
I
292
R
293
E
294
F
295
R
296
Q
297
T
298
F
299
R
300
K
301
I
302
I
303
R
304
S
305
H
306
V
307
L
308
R
309
Q
310
Q
311
E
312
P
313
F
314
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:

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

Xanthine amine congener

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
c16
c17
c18
c19
c20
c21
c22
c23
c24
c25
c26
c27
c28
c29
c30
c31
c32
c33
c34
c35
c36
c37
c38
c39
c40
c41
Pockets
Show nearby residues?
Smoothing window size:
Pocket number Color Mean volume Avg. Polarity Avg. Hydroph. Density Avg. Hydroph. Score Druggability %
Genetic variants
Display
Color by:
Show every atom:
Top disease label:
Filter by aminoacid change:
Filter by functional site:
Filter by predicted impact:
Download

PARTNER SERVERS

GPCRdb

GPCR-ModSim

GPCRM

NMRlipids

HomolWat

Hybrid MM/CG Webserver

CONTACT & LINKS

Documentation

Cite us

Privacy policy

Cookies policy

Disclaimer

Terms & Conditions

SUPPORTED BY

ERNEST (COST Action CA18133)

GLISTEN (COST Action CM1207)