Aggrescan4D: VAPB [mutate: KE3A, EK5A, QE6A, EQ11A, PS12A, QP13A, KT17A, DN24A, TA28A, ND29A, KN31A, PS35A, DH37A, RQ38A, NI39A, CR41A, RL50A, RG51A, PD56A, IV60A, DN62A, AV63A, AT65A, IV67A, SF70A, PR75A, DN77A, YC78A, NS81A, ED82A, HD86A, ML89A, SC92A, AP95A, TA97A, DY98A, DH101A, MT102A, AT104A, EA112A, LV114A, MT115A, KN118A, LM125A, PA126A, NY129A, IV141A, AV145A, TR148A, PS151A, IV152A, VM153A, ST154A, SR158A, LS161A, DN163A, EK165A, KV168A, EV171A, CY173A, GS178A, EK179A, QR181A, RK182A, KT188A, LP196A, RW197A, ML198A, TA201A, QL203A, SG204A, IV208A, SL209A, AD212A, TA214A, GR219A, LR220A, RP223A, LS225A, AD226A, LP227A, LV230A, FL231A, GV235A, IV237A, KR240A, IT241A]

Project name: VAPB [mutate: KE3A, EK5A, QE6A, EQ11A, PS12A, QP13A, KT17A, DN24A, TA28A, ND29A, KN31A, PS35A, DH37A, RQ38A, NI39A, CR41A, RL50A, RG51A, PD56A, IV60A, DN62A, AV63A, AT65A, IV67A, SF70A, PR75A, DN77A, YC78A, NS81A, ED82A, HD86A, ML89A, SC92A, AP95A, TA97A, DY98A, DH101A, MT102A, AT104A, EA112A, LV114A, MT115A, KN118A, LM125A, PA126A, NY129A, IV141A, AV145A, TR148A, PS151A, IV152A, VM153A, ST154A, SR158A, LS161A, DN163A, EK165A, KV168A, EV171A, CY173A, GS178A, EK179A, QR181A, RK182A, KT188A, LP196A, RW197A, ML198A, TA201A, QL203A, SG204A, IV208A, SL209A, AD212A, TA214A, GR219A, LR220A, RP223A, LS225A, AD226A, LP227A, LV230A, FL231A, GV235A, IV237A, KR240A, IT241A]

Status: done

Started: 2026-07-11 22:37:41

Chain sequence(s)	A: MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKIISTTASKTETPIVSKSLSSSLDDTEVKKVMEECKRLQGEVQRLREENKQFKEEDGLRMRKTVQSNSPISALAPTGKEEGLSTRLLALVVLFFIVGVIIGKIAL input PDB
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	No
alphaCutter usage	No
Dynamic mode	Yes
Automated mutations	No
Mutated residues	GV235A,IV237A,LV230A,FL231A,YC78A,DN77A,PR75A,SF70A,AT104A,MT102A,DH101A,LP227A,AD226A,LS225A,RP223A,LR220A,AT65A,IV67A,IV60A,DN62A,AV63A,IT241A,EA112A,MT115A,LV114A,KN118A,RG51A,RL50A,TA214A,PD56A,GR219A,KT188A,RK182A,QR181A,EK165A,SL209A,LS161A,DN163A,SG204A,TA201A,QL203A,ML198A,RW197A,IV208A,CR41A,CY173A,EV171A,EK179A,GS178A,KN31A,DH37A,PS35A,KV168A,NI39A,RQ38A,IV141A,AV145A,TR148A,AD212A,DN24A,TA28A,ND29A,SR158A,DY98A,AP95A,ST154A,TA97A,PS151A,VM153A,SC92A,KT17A,EQ11A,QP13A,PS12A,KE3A,EK5A,QE6A,IV152A,ED82A,KR240A,NS81A,HD86A,ML89A,NY129A,LM125A,PA126A,LP196A
Energy difference between WT (input) and mutated protein (by FoldX)	55.5463 kcal/mol CAUTION: Your mutation/s can destabilize the protein structure
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Simulation log

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[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:03:49)
[INFO]       CABS:     Running CABS flex simulation                                                (00:29:53)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:56:17)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:56:18)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:56:19)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:56:19)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:56:20)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:56:21)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:56:22)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:56:23)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:56:24)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:56:25)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:56:25)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:56:26)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:56:27)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:56:30)
[INFO]       Main:     Simulation completed successfully.                                          (00:56:31)

Note Your prediction results will be deleted after 360 days.

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Show buried residues

Minimal score value: -4.4142
Maximal score value: 6.3092
Average score: -0.5617
Total score value: -136.4982

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	M	A	0.3860
2	A	A	-0.8465
3	E	A	-2.0333	mutated: KE3A
4	V	A	-1.4325
5	K	A	-2.7956	mutated: EK5A
6	E	A	-2.8278	mutated: QE6A
7	V	A	0.0000
8	L	A	0.0000
9	S	A	-1.1687
10	L	A	-1.0478
11	Q	A	-1.8268	mutated: EQ11A
12	S	A	-1.4262	mutated: PS12A
13	P	A	0.0000	mutated: QP13A
14	H	A	-1.7795
15	E	A	-2.0305
16	L	A	0.0000
17	T	A	0.0000	mutated: KT17A
18	F	A	0.0000
19	R	A	-0.2426
20	G	A	-0.2817
21	P	A	0.0000
22	F	A	-0.1537
23	T	A	-0.4604
24	N	A	-1.0882	mutated: DN24A
25	V	A	-0.5118
26	V	A	0.0000
27	T	A	0.0000
28	A	A	0.0000	mutated: TA28A
29	D	A	-0.8072	mutated: ND29A
30	L	A	0.0000
31	N	A	-1.4322	mutated: KN31A
32	L	A	0.0000
33	G	A	-0.8035
34	N	A	0.0000
35	S	A	-0.6234	mutated: PS35A
36	T	A	-1.0531
37	H	A	-1.3372	mutated: DH37A
38	Q	A	-0.4278	mutated: RQ38A
39	I	A	0.0000	mutated: NI39A
40	V	A	0.0000
41	R	A	0.0000	mutated: CR41A
42	F	A	0.0000
43	K	A	-1.0219
44	V	A	0.0000
45	K	A	-1.5000
46	T	A	-1.0763
47	T	A	-0.8245
48	A	A	-0.2188
49	P	A	0.2121
50	L	A	0.5773	mutated: RL50A
51	G	A	0.2009	mutated: RG51A
52	Y	A	0.2008
53	C	A	0.0254
54	V	A	0.0000
55	R	A	0.0000
56	D	A	0.0000	mutated: PD56A
57	N	A	-0.9018
58	S	A	0.0000
59	G	A	0.0000
60	V	A	0.0000	mutated: IV60A
61	I	A	0.0000
62	N	A	0.2414	mutated: DN62A
63	V	A	1.1086	mutated: AV63A
64	G	A	-0.0482
65	T	A	0.0000	mutated: AT65A
66	S	A	-0.4469
67	V	A	0.0000	mutated: IV67A
68	N	A	-0.5252
69	V	A	0.0000
70	F	A	0.0000	mutated: SF70A
71	V	A	0.0000
72	M	A	-0.1308
73	L	A	0.0000
74	Q	A	-0.7179
75	R	A	0.0000	mutated: PR75A
76	F	A	0.5326
77	N	A	-1.0812	mutated: DN77A
78	C	A	0.0000	mutated: YC78A
79	D	A	-2.5164
80	P	A	-2.1417
81	S	A	-1.9431	mutated: NS81A
82	D	A	-3.1284	mutated: ED82A
83	K	A	-2.8607
84	S	A	-1.8706
85	K	A	-1.7309
86	D	A	0.0000	mutated: HD86A
87	K	A	-1.7480
88	F	A	0.0000
89	L	A	-0.6990	mutated: ML89A
90	V	A	0.0000
91	Q	A	-0.4315
92	C	A	0.0000	mutated: SC92A
93	M	A	0.0000
94	F	A	-0.5696
95	P	A	0.0000	mutated: AP95A
96	P	A	0.1786
97	A	A	0.7030	mutated: TA97A
98	Y	A	1.1602	mutated: DY98A
99	T	A	0.2758
100	S	A	0.0000
101	H	A	-1.1962	mutated: DH101A
102	T	A	0.0000	mutated: MT102A
103	E	A	-2.0379
104	T	A	-1.5116	mutated: AT104A
105	V	A	0.0000
106	W	A	-1.0255
107	K	A	-2.2979
108	E	A	-1.8363
109	A	A	-1.5157
110	K	A	-1.6878
111	P	A	-0.8409
112	A	A	-0.6617	mutated: EA112A
113	D	A	-1.3153
114	V	A	0.1530	mutated: LV114A
115	T	A	0.0000	mutated: MT115A
116	D	A	-1.1684
117	S	A	0.0000
118	N	A	-1.4911	mutated: KN118A
119	L	A	0.0000
120	R	A	-1.8771
121	C	A	0.0000
122	V	A	0.0000
123	F	A	0.0000
124	E	A	-1.1061
125	M	A	-0.6154	mutated: LM125A
126	A	A	-0.3858	mutated: PA126A
127	A	A	-0.4744
128	E	A	-0.7134
129	Y	A	-0.2251	mutated: NY129A
130	D	A	0.0000
131	K	A	0.0000
132	P	A	-0.3036
133	H	A	0.0815
134	D	A	0.0474
135	V	A	0.0000
136	E	A	0.0000
137	I	A	2.1017
138	N	A	1.1263
139	K	A	0.0000
140	I	A	2.2299
141	V	A	0.0000	mutated: IV141A
142	S	A	-0.2443
143	T	A	0.0815
144	T	A	0.5244
145	V	A	0.6982	mutated: AV145A
146	S	A	-0.4537
147	K	A	-1.8283
148	R	A	-2.9849	mutated: TR148A
149	E	A	-2.9867
150	T	A	-1.9214
151	S	A	-1.3639	mutated: PS151A
152	V	A	0.0000	mutated: IV152A
153	M	A	0.1009	mutated: VM153A
154	T	A	0.2053	mutated: ST154A
155	K	A	-0.1274
156	S	A	-0.0254
157	L	A	-0.0289
158	R	A	-1.9519	mutated: SR158A
159	S	A	-1.8774
160	S	A	-1.7422
161	S	A	-1.4111	mutated: LS161A
162	D	A	-2.3561
163	N	A	-2.6689	mutated: DN163A
164	T	A	-1.9252
165	K	A	-2.5901	mutated: EK165A
166	V	A	-1.7217
167	K	A	-1.6782
168	V	A	-0.4646	mutated: KV168A
169	V	A	0.0000
170	M	A	-0.0964
171	V	A	-0.1149	mutated: EV171A
172	E	A	-1.9400
173	Y	A	-0.8751	mutated: CY173A
174	K	A	-2.1572
175	R	A	-2.9768
176	L	A	-1.3772
177	Q	A	-2.3304
178	S	A	-2.5842	mutated: GS178A
179	K	A	-1.9708	mutated: EK179A
180	V	A	-1.9051
181	R	A	-3.6439	mutated: QR181A
182	K	A	-3.4786	mutated: RK182A
183	L	A	0.0000
184	R	A	-3.1286
185	E	A	-3.8760
186	E	A	-3.3946
187	N	A	0.0000
188	T	A	-2.7105	mutated: KT188A
189	Q	A	-3.3095
190	F	A	-2.1027
191	K	A	-2.4143
192	E	A	-3.0757
193	E	A	-2.5270
194	D	A	0.0000
195	G	A	-1.7128
196	P	A	-1.5890	mutated: LP196A
197	W	A	-0.5929	mutated: RW197A
198	L	A	-0.0844	mutated: ML198A
199	R	A	-1.9363
200	K	A	-1.7475
201	A	A	-0.6837	mutated: TA201A
202	V	A	-0.0856
203	L	A	0.0000	mutated: QL203A
204	G	A	0.0000	mutated: SG204A
205	N	A	-0.9130
206	S	A	-0.4315
207	P	A	-0.3437
208	V	A	-0.1855	mutated: IV208A
209	L	A	-0.0077	mutated: SL209A
210	A	A	0.0000
211	L	A	0.0000
212	D	A	0.0000	mutated: AD212A
213	P	A	0.0000
214	A	A	-1.1104	mutated: TA214A
215	G	A	-2.4215
216	K	A	-3.8113
217	E	A	-4.1210
218	E	A	-4.4111
219	R	A	-4.4142	mutated: GR219A
220	R	A	-3.8033	mutated: LR220A
221	S	A	-2.2516
222	T	A	-2.1227
223	P	A	-1.2360	mutated: RP223A
224	L	A	-0.0889
225	S	A	-0.1541	mutated: LS225A
226	D	A	-0.3513	mutated: AD226A
227	P	A	1.1893	mutated: LP227A
228	V	A	2.6626
229	V	A	3.6852
230	V	A	4.2749	mutated: LV230A
231	L	A	5.2115	mutated: FL231A
232	F	A	6.1167
233	I	A	6.3092
234	V	A	5.6500
235	V	A	5.5965	mutated: GV235A
236	V	A	4.5539
237	V	A	4.0222	mutated: IV237A
238	I	A	3.2853
239	G	A	1.3982
240	R	A	-0.6189	mutated: KR240A
241	T	A	0.1256	mutated: IT241A
242	A	A	0.7579
243	L	A	1.9403

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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, -0.5617 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_1	-0.5617	View	CSV	PDB
model_3	-0.6198	View	CSV	PDB
model_11	-0.6226	View	CSV	PDB
model_5	-0.6269	View	CSV	PDB
model_7	-0.6279	View	CSV	PDB
model_2	-0.6453	View	CSV	PDB
CABS_average	-0.6579	View	CSV	PDB
model_4	-0.6583	View	CSV	PDB
model_0	-0.667	View	CSV	PDB
model_10	-0.6846	View	CSV	PDB
model_6	-0.7085	View	CSV	PDB
model_9	-0.7188	View	CSV	PDB
model_8	-0.7532	View	CSV	PDB
input	-0.7783	View	CSV	PDB

Status: done

Started: 2026-07-11 22:37:41

CABS-flex predictions of flexibility of input structure

Model

Average A4D Score