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GPCRmd Workbench

How to
use it
Show info

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

human smoothened receptor (4QIN) 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
Q
192
C
193
E
194
V
195
P
196
L
197
V
198
R
199
T
200
D
201
N
202
P
203
K
204
S
205
W
206
Y
207
E
208
D
209
V
210
E
211
G
212
C
213
G
214
I
215
Q
216
C
217
Q
218
N
219
P
220
L
221
F
222
T
223
E
224
A
225
E
226
H
227
Q
228
D
229
M
230
H
231
S
232
Y
233
I
234
A
235
A
236
F
237
G
238
A
239
V
240
T
241
G
242
L
243
C
244
T
245
L
246
F
247
T
248
L
249
A
250
T
251
F
252
V
253
A
254
D
255
W
256
R
257
N
258
S
259
N
260
R
261
Y
262
P
263
A
264
V
265
I
266
L
267
F
268
Y
269
V
270
N
271
A
272
C
273
F
274
F
275
V
276
G
277
S
278
I
279
G
280
W
281
L
282
A
283
Q
284
F
285
M
286
D
287
G
288
A
289
R
290
R
291
E
292
I
293
V
294
C
295
R
296
A
297
D
298
G
299
T
300
M
301
R
302
L
303
G
304
E
305
P
306
T
307
S
308
N
309
E
310
T
311
L
312
S
313
C
314
V
315
I
316
I
317
F
318
V
319
I
320
V
321
Y
322
Y
323
A
324
L
325
M
326
A
327
G
328
V
329
V
330
W
331
F
332
V
333
V
334
L
335
T
336
Y
337
A
338
W
339
H
340
T
341
S
342
F
343
K
344
A
345
L
346
G
347
T
348
T
349
Y
350
Q
351
P
352
L
353
S
354
G
355
K
356
T
357
S
358
Y
359
F
360
H
361
L
362
L
363
T
364
W
365
S
366
L
367
P
368
F
369
V
370
L
371
T
372
V
373
A
374
I
375
L
376
A
377
V
378
A
379
Q
380
V
381
D
382
G
383
D
384
S
385
V
386
S
387
G
388
I
389
C
390
F
391
V
392
G
393
Y
394
K
395
N
396
Y
397
R
398
Y
399
R
400
A
401
G
402
F
403
V
404
L
405
A
406
P
407
I
408
G
409
L
410
V
411
L
412
I
413
V
414
G
415
G
416
Y
417
F
418
L
419
I
420
R
421
G
422
V
423
M
424
T
425
L
426
F
427
S
428
I
429
K
430
S
431
N
432
H
433
P
434
G
435
L
436
L
437
S
438
E
439
K
440
A
441
A
442
S
443
K
444
I
445
N
446
E
447
T
448
M
449
L
450
R
451
L
452
G
453
I
454
F
455
G
456
F
457
L
458
A
459
F
460
G
461
F
462
V
463
L
464
I
465
T
466
F
467
S
468
C
469
H
470
F
471
Y
472
D
473
F
474
F
475
N
476
Q
477
A
478
E
479
W
480
E
481
R
482
S
483
F
484
R
485
D
486
Y
487
V
488
L
489
C
490
Q
491
A
492
N
493
V
494
T
495
I
496
G
497
L
498
P
499
T
500
K
501
Q
502
P
503
I
504
P
505
D
506
C
507
E
508
I
509
K
510
N
511
R
512
P
513
S
514
L
515
L
516
V
517
E
518
K
519
I
520
N
521
L
522
F
523
A
524
M
525
F
526
G
527
T
528
G
529
I
530
A
531
M
532
S
533
T
534
W
535
V
536
W
537
T
538
K
539
A
540
T
541
L
542
L
543
I
544
W
545
R
546
R
547
T
548
W
549
C
550
R
551
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
Q
192
C
193
E
194
V
195
P
196
L
197
V
198
R
199
T
200
D
201
N
202
P
203
K
204
S
205
W
206
Y
207
E
208
D
209
V
210
E
211
G
212
C
213
G
214
I
215
Q
216
C
217
Q
218
N
219
P
220
L
221
F
222
T
223
E
224
A
225
E
226
H
227
Q
228
D
229
M
230
H
231
S
232
Y
233
I
234
A
235
A
236
F
237
G
238
A
239
V
240
T
241
G
242
L
243
C
244
T
245
L
246
F
247
T
248
L
249
A
250
T
251
F
252
V
253
A
254
D
255
W
256
R
257
N
258
S
259
N
260
R
261
Y
262
P
263
A
264
V
265
I
266
L
267
F
268
Y
269
V
270
N
271
A
272
C
273
F
274
F
275
V
276
G
277
S
278
I
279
G
280
W
281
L
282
A
283
Q
284
F
285
M
286
D
287
G
288
A
289
R
290
R
291
E
292
I
293
V
294
C
295
R
296
A
297
D
298
G
299
T
300
M
301
R
302
L
303
G
304
E
305
P
306
T
307
S
308
N
309
E
310
T
311
L
312
S
313
C
314
V
315
I
316
I
317
F
318
V
319
I
320
V
321
Y
322
Y
323
A
324
L
325
M
326
A
327
G
328
V
329
V
330
W
331
F
332
V
333
V
334
L
335
T
336
Y
337
A
338
W
339
H
340
T
341
S
342
F
343
K
344
A
345
L
346
G
347
T
348
T
349
Y
350
Q
351
P
352
L
353
S
354
G
355
K
356
T
357
S
358
Y
359
F
360
H
361
L
362
L
363
T
364
W
365
S
366
L
367
P
368
F
369
V
370
L
371
T
372
V
373
A
374
I
375
L
376
A
377
V
378
A
379
Q
380
V
381
D
382
G
383
D
384
S
385
V
386
S
387
G
388
I
389
C
390
F
391
V
392
G
393
Y
394
K
395
N
396
Y
397
R
398
Y
399
R
400
A
401
G
402
F
403
V
404
L
405
A
406
P
407
I
408
G
409
L
410
V
411
L
412
I
413
V
414
G
415
G
416
Y
417
F
418
L
419
I
420
R
421
G
422
V
423
M
424
T
425
L
426
F
427
S
428
I
429
K
430
S
431
N
432
H
433
P
434
G
435
L
436
L
437
S
438
E
439
K
440
A
441
A
442
S
443
K
444
I
445
N
446
E
447
T
448
M
449
L
450
R
451
L
452
G
453
I
454
F
455
G
456
F
457
L
458
A
459
F
460
G
461
F
462
V
463
L
464
I
465
T
466
F
467
S
468
C
469
H
470
F
471
Y
472
D
473
F
474
F
475
N
476
Q
477
A
478
E
479
W
480
E
481
R
482
S
483
F
484
R
485
D
486
Y
487
V
488
L
489
C
490
Q
491
A
492
N
493
V
494
T
495
I
496
G
497
L
498
P
499
T
500
K
501
Q
502
P
503
I
504
P
505
D
506
C
507
E
508
I
509
K
510
N
511
R
512
P
513
S
514
L
515
L
516
V
517
E
518
K
519
I
520
N
521
L
522
F
523
A
524
M
525
F
526
G
527
T
528
G
529
I
530
A
531
M
532
S
533
T
534
W
535
V
536
W
537
T
538
K
539
A
540
T
541
L
542
L
543
I
544
W
545
R
546
R
547
T
548
W
549
C
550
R
551
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: %
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
Water volume distribution
Display map
Map style
Opacity
1
Smoothness
10
ISO level
1
Show Polar residues
Show waters within
Å of protein
Tunnels and channels
Clusters Highest throughput
Style -
c1
c2
c3
c4
c5
c6
c7
c8
c9
c10
c11
c12
c13
c14
Pockets
Show nearby residues?
Smoothing window size:
Pocket number Color Mean volume Avg. Polarity Avg. Hydroph. Density Avg. Hydroph. Score Druggability %