Project name: 1bj1

Status: done

Started: 2024-04-23 21:52:44
Chain sequence(s) H: EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
L: DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
input PDB
Selected Chain(s) H,L
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:10)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:10)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:10)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:10)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:10)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:16)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:06:43)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:06:45)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:06:47)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:06:50)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:06:52)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:06:54)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:06:56)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:06:58)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:07:00)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:07:02)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:07:04)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:07:06)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:07:08)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:07:16)
[INFO]       Main:     Simulation completed successfully.                                          (01:07:18)
Show buried residues
Minimal score value
-3.6167
Maximal score value
2.7244
Average score
-0.5172
Total score value
-222.931
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 D L -2.1676
2 I L 0.0000
3 Q L -1.5848
4 M L -0.7336
5 T L -0.4520
6 Q L -0.5509
7 S L -0.4095
8 P L -0.5290
9 S L -0.6536
10 S L -0.8181
11 L L 0.0000
12 S L -0.6365
13 A L -0.7861
14 S L -0.4236
15 V L 0.1681
16 G L -0.9740
17 D L -2.4415
18 R L -2.5894
19 V L -1.1621
20 T L -0.6772
21 I L 0.0000
22 T L -0.3956
23 C L 0.0000
24 S L -0.8288
25 A L 0.0000
26 S L -2.0080
27 Q L -2.6006
28 D L -2.9361
29 I L 0.0000
30 S L -1.2401
31 N L -0.8556
32 Y L 0.2345
33 L L 0.0000
34 N L 0.0000
35 W L 0.0000
36 Y L 0.0000
37 Q L 0.0000
38 Q L 0.0000
39 K L -2.3407
40 P L -1.5589
41 G L -1.2770
42 K L -1.5530
43 A L 0.0000
44 P L 0.0000
45 K L -1.2015
46 V L 0.0000
47 L L 0.0000
48 I L 0.0000
49 Y L 0.0000
50 F L 0.2586
51 T L 0.0376
52 S L 0.2839
53 S L 0.2097
54 L L 0.5584
55 H L -0.5070
56 S L -0.4250
57 G L -0.5910
58 V L -0.3688
59 P L -0.6326
60 S L -0.7531
61 R L -0.9122
62 F L 0.0000
63 S L -0.1803
64 G L -0.2088
65 S L -0.5660
66 G L -0.7922
67 S L -1.0003
68 G L -1.4899
69 T L -1.7200
70 D L -1.6470
71 F L 0.0000
72 T L -0.4815
73 L L 0.0000
74 T L -0.6775
75 I L 0.0000
76 S L -1.5428
77 S L -1.2014
78 L L 0.0000
79 Q L -1.8583
80 P L -1.9214
81 E L -1.7342
82 D L -2.3209
83 F L 0.0000
84 A L 0.0000
85 T L 0.0000
86 Y L 0.0000
87 Y L 0.0000
88 C L 0.0000
89 Q L 0.0000
90 Q L 0.0000
91 Y L 0.0000
92 S L -0.3192
93 T L 0.7233
94 V L 1.4260
95 P L 0.6210
96 W L 0.0000
97 T L 0.0000
98 F L -0.0914
99 G L -0.4502
100 Q L 0.0000
101 G L -0.6111
102 T L 0.0000
103 K L -1.1428
104 V L 0.0000
105 E L -1.2367
106 I L 0.0000
107 K L 0.0000
108 R L -1.2419
109 T L -0.2412
110 V L 1.0715
111 A L 0.0000
112 A L 0.2388
113 P L 0.3591
114 S L 0.2015
115 V L 0.7598
116 F L 0.0000
117 I L 0.3646
118 F L 0.0000
119 P L 0.0000
120 P L -0.4579
121 S L -1.3002
122 D L -2.2791
123 E L -1.8687
124 Q L 0.0000
125 L L -1.1672
126 K L -2.1937
127 S L -1.4354
128 G L -1.0812
129 T L 0.0000
130 A L 0.0000
131 S L 0.0000
132 V L 0.0000
133 V L 0.0000
134 C L 0.0000
135 L L 0.0000
136 L L 0.0000
137 N L 0.0000
138 N L -0.4413
139 F L 0.0000
140 Y L -0.6105
141 P L -1.1361
142 R L -2.0558
143 E L -2.3161
144 A L -1.9371
145 K L -2.3642
146 V L -1.7218
147 Q L -1.7723
148 W L 0.0000
149 K L -1.4335
150 V L 0.0000
151 D L -2.9670
152 N L -2.0967
153 A L -0.6165
154 L L 0.2743
155 Q L -0.3483
156 S L -0.5830
157 G L -1.1102
158 N L -1.4806
159 S L -0.6927
160 Q L 0.0000
161 E L -1.3123
162 S L -0.1816
163 V L 0.2626
164 T L 0.0000
165 E L -1.4383
166 Q L 0.0000
167 D L -2.9169
168 S L -2.2060
169 K L -2.8978
170 D L -2.7706
171 S L -2.4597
172 T L 0.0000
173 Y L -0.9903
174 S L 0.0000
175 L L 0.0000
176 S L 0.0000
177 S L -0.7807
178 T L 0.0000
179 L L 0.0000
180 T L -0.6150
181 L L 0.0000
182 S L -0.9160
183 K L -1.5967
184 A L -1.3235
185 D L -1.9656
186 Y L -1.9948
187 E L -2.5592
188 K L -3.1582
189 H L 0.0000
190 K L -3.6167
191 V L -2.0882
192 Y L 0.0000
193 A L -1.1026
194 C L 0.0000
195 E L -1.9486
196 V L 0.0000
197 T L -1.3903
198 H L 0.0000
199 Q L -1.8081
200 G L -0.8261
201 L L 0.0241
202 S L -0.5043
203 S L -0.3818
204 P L -0.7276
205 V L -0.0833
206 T L -0.2966
207 K L 0.0000
208 S L -0.3981
209 F L -0.6715
210 N L -2.1405
211 R L -2.8622
212 G L -2.7726
213 E L -2.7622
1 E H -2.0682
2 V H 0.0000
3 Q H -1.3808
4 L H 0.0000
5 V H 0.7426
6 E H 0.0000
7 S H -0.3117
8 G H -0.7095
9 G H -0.6672
10 G H -0.4058
11 L H 0.0706
12 V H -0.4350
13 Q H -1.2529
14 P H -1.0091
15 G H -1.0386
16 G H -1.0488
17 S H -0.9831
18 L H -0.9779
19 R H -1.9363
20 L H 0.0000
21 S H 0.0000
22 C H 0.0000
23 A H -0.0244
24 A H 0.0000
25 S H -0.3011
26 G H -0.4461
27 Y H 0.4677
28 T H 0.0000
29 F H 0.0000
30 T H -0.5083
31 N H -0.7342
32 Y H 0.1188
33 G H 0.0000
34 M H 0.0000
35 N H 0.0000
36 W H 0.0000
37 V H 0.0000
38 R H -0.4035
39 Q H 0.0000
40 A H -0.8499
41 P H -1.1666
42 G H -1.1019
43 K H 0.0000
44 G H -0.3597
45 L H 0.0000
46 E H 0.0000
47 W H 0.0000
48 V H 0.0000
49 G H 0.0000
50 W H 0.0690
51 I H 0.0000
52 N H -0.2049
53 T H 0.0095
54 Y H 0.7386
55 T H -0.1199
56 G H -0.7717
57 E H -1.3576
58 P H -0.2612
59 T H 0.3110
60 Y H 0.3065
61 A H 0.2315
62 A H -0.6405
63 D H -1.8099
64 F H 0.0000
65 K H -2.6279
66 R H -2.7480
67 R H 0.0000
68 F H 0.3271
69 T H 0.7360
70 F H 1.0608
71 S H 0.9219
72 L H 1.0816
73 D H -0.3583
74 T H -0.7129
75 S H -1.1177
76 K H -1.5588
77 S H -0.5987
78 T H 0.0000
79 A H 0.0000
80 Y H 0.1460
81 L H 0.0000
82 Q H -0.4758
83 M H 0.0000
84 N H -1.2906
85 S H -1.0458
86 L H -1.0482
87 R H -1.3511
88 A H -0.8038
89 E H -1.2207
90 D H -1.9938
91 T H 0.0000
92 A H 0.0000
93 V H 0.0000
94 Y H 0.0000
95 Y H 0.0000
96 C H 0.0000
97 A H 0.0000
98 K H 0.0000
99 Y H 0.0000
100 P H -0.1999
101 H H 0.4052
102 Y H 1.6027
103 Y H 1.6314
104 G H 0.5443
105 S H 0.4239
106 S H 0.5487
107 H H 0.0000
108 W H 0.5920
109 Y H 0.0000
110 F H 0.0000
111 D H -0.9699
112 V H 0.0000
113 W H 0.0000
114 G H -0.3859
115 Q H 0.0000
116 G H -0.5847
117 T H 0.0000
118 L H -0.4414
119 V H 0.0000
120 T H 0.0000
121 V H -0.1874
122 S H -0.4242
123 S H -0.2744
124 A H -0.2407
125 S H -0.3899
126 T H -0.5858
127 K H -1.1134
128 G H -0.8825
129 P H -0.4430
130 S H -0.2959
131 V H -0.3831
132 F H 0.0000
133 P H -1.1050
134 L H 0.0000
135 A H 0.0000
136 P H -0.9399
137 S H -0.6721
144 G H -0.7863
145 T H -0.4228
146 A H 0.0000
147 A H 0.0000
148 L H 0.0000
149 G H 0.0000
150 C H 0.0000
151 L H 0.0000
152 V H 0.0000
153 K H 0.0000
154 D H 0.0856
155 Y H 0.0000
156 F H 0.0000
157 P H -0.3643
158 E H -0.8351
159 P H -0.7176
160 V H 0.0000
161 T H -0.3576
162 V H 0.0000
163 S H -0.3728
164 W H -0.6408
165 N H -1.5731
166 S H -0.4918
167 G H 0.0286
168 A H 0.4147
169 L H 0.9617
170 T H 0.4194
171 S H -0.2541
172 G H 0.0000
173 V H 0.2712
174 H H 0.0000
175 T H 0.2845
176 F H 0.4888
177 P H 0.8141
178 A H 0.0000
179 V H 2.7244
180 L H 2.1882
181 Q H 0.0000
182 S H -0.1730
183 S H 0.0583
184 G H 0.0000
185 L H 2.3783
186 Y H 2.3430
187 S H 0.0000
188 L H 0.9990
189 S H 0.0000
190 S H 0.0000
191 V H 0.0000
192 V H 0.0000
193 T H 0.0000
194 V H 0.4587
195 P H 0.0466
196 S H -0.2463
197 S H -0.2160
198 S H -0.3085
199 L H -0.0407
200 G H -0.4913
201 T H -0.8320
202 Q H 0.0000
203 T H -0.8639
204 Y H 0.0000
205 I H -1.5236
206 C H 0.0000
207 N H -1.8732
208 V H 0.0000
209 N H -1.7701
210 H H 0.0000
211 K H -2.2644
212 P H -1.3661
213 S H -1.6819
214 N H -2.3091
215 T H -2.1201
216 K H -2.6295
217 V H -1.6477
218 D H -2.8832
219 K H -2.6896
220 K H -2.5701
221 V H 0.0000
222 E H -2.0398
223 P H -1.5966
224 K H -2.1667
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.5172 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_5 -0.5172 View CSV PDB
model_7 -0.5177 View CSV PDB
model_0 -0.5346 View CSV PDB
model_10 -0.5445 View CSV PDB
model_6 -0.5458 View CSV PDB
model_3 -0.546 View CSV PDB
model_2 -0.5594 View CSV PDB
CABS_average -0.5655 View CSV PDB
model_4 -0.5731 View CSV PDB
model_11 -0.596 View CSV PDB
model_8 -0.6022 View CSV PDB
model_9 -0.6118 View CSV PDB
model_1 -0.6372 View CSV PDB
input -0.711 View CSV PDB