Project name: 5B5 MUTANT ANTIBODY 11

Status: done

Started: 2026-03-17 05:35:45
Chain sequence(s) A: DIVMTQTPLSLPVTPGEPASISCRSSQSLVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage Used: no changes made
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:12)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:12)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:12)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:22)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/348dad16975792f/tmp/folded.pdb                (00:03:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:46)
Show buried residues
Minimal score value
-3.1588
Maximal score value
1.7169
Average score
-0.6259
Total score value
-152.0886
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 A -1.0342
2 I A 0.0000
3 V A 0.7645
4 M A 0.0000
5 T A -0.2869
6 Q A 0.0000
7 T A -0.0636
8 P A 0.4260
9 L A 1.2127
10 S A 0.0564
11 L A -0.3535
12 P A -1.2997
13 V A 0.0000
14 T A -1.7595
15 P A -2.0449
16 G A -1.9320
17 E A -2.3750
18 P A -2.2337
19 A A 0.0000
20 S A -0.8715
21 I A 0.0000
22 S A -0.9109
23 C A 0.0000
24 R A -2.2843
25 S A 0.0000
26 S A -1.0066
27 Q A -1.5661
28 S A -0.9268
29 L A 0.0000
30 V A 0.3481
31 H A -0.5533
32 S A -0.8843
33 N A -1.5894
34 G A -1.0184
35 N A -0.7456
36 T A -0.1905
37 Y A 0.0628
38 L A 0.0000
39 E A -0.0528
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A -0.9099
44 K A -1.6545
45 P A -1.1701
46 G A -1.5295
47 Q A -2.1200
48 S A -1.2656
49 P A 0.0000
50 Q A -1.0308
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A 0.0280
55 K A -0.2157
56 L A -0.1898
57 S A -0.0426
58 Y A 0.6076
59 R A -0.8677
60 A A 0.0000
61 S A -0.5097
62 G A -1.0611
63 V A -0.8872
64 P A -1.3541
65 D A -2.2699
66 R A -2.2207
67 F A 0.0000
68 S A -1.2559
69 G A 0.0000
70 S A -0.7629
71 G A -1.0501
72 S A -0.7302
73 G A -0.7042
74 T A -1.4636
75 D A -2.1009
76 F A 0.0000
77 T A -1.1565
78 L A 0.0000
79 K A -2.1376
80 I A 0.0000
81 S A -2.4186
82 R A -3.1588
83 V A 0.0000
84 E A -2.5407
85 A A -1.9095
86 E A -2.5620
87 D A 0.0000
88 V A -1.2892
89 G A 0.0000
90 V A -0.1557
91 Y A 0.0000
92 Y A 0.0000
93 C A 0.0000
94 F A 0.0000
95 Q A 0.0000
96 G A 0.2208
97 S A 0.0000
98 H A 0.0624
99 V A 1.4403
100 P A 0.6664
101 F A 0.7168
102 T A 0.3936
103 F A 0.3553
104 G A 0.0000
105 S A -0.0355
106 G A 0.0000
107 T A 0.0000
108 K A -0.6407
109 L A 0.0000
110 E A -1.9523
111 I A -2.0011
112 K A -2.4431
113 G A -1.7665
114 G A -1.6360
115 G A -1.4329
116 G A -1.7431
117 S A -1.2336
118 G A -1.7240
119 G A -1.6397
120 G A -1.7431
121 G A -1.6652
122 S A -1.0680
123 G A -1.2932
124 G A -1.2554
125 G A -1.1795
126 G A -1.0012
127 S A -0.9582
128 V A 0.0000
129 Q A -1.3570
130 L A 0.0000
131 V A 0.1966
132 Q A 0.0000
133 S A -0.5934
134 G A -0.6580
135 A A -0.1371
136 E A -0.2767
137 V A 0.8116
138 K A -0.9602
139 K A -2.1618
140 P A -2.2607
141 G A -1.6028
142 A A -1.2460
143 S A -1.3202
144 V A 0.0000
145 K A -1.8499
146 V A 0.0000
147 S A -0.6148
148 C A 0.0000
149 K A -0.9387
150 A A 0.0000
151 S A -0.7356
152 G A -0.8329
153 Y A -0.5742
154 T A -0.6095
155 F A 0.0000
156 T A -0.1441
157 D A -1.4412
158 Y A -0.7150
159 I A 0.0490
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 R A 0.0000
165 Q A -0.5738
166 A A -1.0126
167 P A -1.0238
168 G A -1.2133
169 Q A -1.6776
170 G A -0.9515
171 L A 0.0000
172 E A -0.4858
173 W A 0.0000
174 M A 0.0000
175 G A 0.0000
176 N A -0.3000
177 I A 0.0000
178 D A 0.1441
179 P A 0.0000
180 Y A 1.4017
181 Y A 1.7169
182 G A 0.4575
183 S A 0.1572
184 T A -0.0964
185 G A 0.0524
186 Y A -0.0590
187 A A 0.0000
188 L A 0.0426
189 K A -1.5419
190 F A 0.0000
191 K A -1.9565
192 G A -1.5102
193 R A -1.4164
194 V A 0.0000
195 T A -0.8757
196 M A 0.0000
197 T A -0.7267
198 R A -1.0221
199 D A -1.3177
200 T A -0.5749
201 S A -0.5991
202 T A -0.6947
203 S A -0.7829
204 T A 0.0000
205 V A 0.0000
206 Y A -0.8077
207 M A 0.0000
208 E A -1.4025
209 L A 0.0000
210 S A -1.1303
211 S A -1.2547
212 L A 0.0000
213 R A -3.1264
214 S A -2.4074
215 E A -2.5869
216 D A 0.0000
217 T A -0.8543
218 A A 0.0000
219 V A 0.2017
220 Y A 0.0000
221 Y A 0.0000
222 C A 0.0000
223 A A 0.0000
224 R A 0.0000
225 D A -1.3413
226 G A -1.1129
227 N A -1.1804
228 Y A -0.2087
229 G A -0.5395
230 S A 0.0000
231 D A -0.6933
232 Y A -0.6063
233 W A -0.5301
234 G A 0.0000
235 Q A -1.3088
236 G A -0.5683
237 T A 0.0000
238 T A -0.0226
239 V A 0.0000
240 T A -0.3629
241 V A 0.0000
242 S A -1.0963
243 S A -1.0065
Download PDB file
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Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.5706 1.9523 View CSV PDB
4.5 -0.6084 1.8815 View CSV PDB
5.0 -0.6529 1.7858 View CSV PDB
5.5 -0.6945 1.6763 View CSV PDB
6.0 -0.7238 1.5867 View CSV PDB
6.5 -0.7351 1.569 View CSV PDB
7.0 -0.7301 1.5515 View CSV PDB
7.5 -0.7146 1.5346 View CSV PDB
8.0 -0.6937 1.5192 View CSV PDB
8.5 -0.6682 1.5061 View CSV PDB
9.0 -0.6378 1.5166 View CSV PDB