Project name: 5B5 MUTANT ANTIBODY 9

Status: done

Started: 2026-03-17 05:34:07
Chain sequence(s) A: DIVMTQTPLSLPVTPGEPASISCRSSQSLVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:08)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:09)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:09)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:52)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/50914d758846683/tmp/folded.pdb                (00:02:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:13)
Show buried residues
Minimal score value
-3.2258
Maximal score value
1.7264
Average score
-0.6294
Total score value
-152.9392
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 -1.0195
2 I A 0.0000
3 V A 0.7731
4 M A 0.0000
5 T A -0.2530
6 Q A 0.0000
7 T A -0.0542
8 P A 0.3814
9 L A 1.1703
10 S A 0.0120
11 L A -0.3526
12 P A -1.2451
13 V A 0.0000
14 T A -1.6076
15 P A -1.9543
16 G A -1.7936
17 E A -2.0443
18 P A -2.0736
19 A A 0.0000
20 S A -0.8712
21 I A 0.0000
22 S A -0.9067
23 C A 0.0000
24 R A -2.1970
25 S A 0.0000
26 S A -0.9908
27 Q A -1.5462
28 S A -0.9204
29 L A 0.0000
30 V A 0.1951
31 H A -0.6418
32 S A -0.9528
33 N A -1.6362
34 G A -1.0861
35 N A -0.8254
36 T A -0.2462
37 Y A 0.0868
38 L A 0.0000
39 E A 0.0000
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A -0.8987
44 K A -1.5497
45 P A -1.1854
46 G A -1.4755
47 Q A -2.1159
48 S A -1.3139
49 P A 0.0000
50 Q A -1.1416
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A 0.2099
55 K A -0.1962
56 L A -0.1362
57 S A 0.0390
58 Y A 0.7239
59 R A -0.7565
60 F A -0.0701
61 S A -0.3954
62 G A -1.0009
63 V A 0.0000
64 P A -1.3291
65 D A -2.4341
66 R A -2.1644
67 F A 0.0000
68 S A -1.2652
69 G A -0.6791
70 S A -0.7792
71 G A -1.0591
72 S A -0.7583
73 G A -0.7475
74 T A -1.5014
75 D A -2.1932
76 F A 0.0000
77 T A -1.1721
78 L A 0.0000
79 K A -2.1119
80 I A 0.0000
81 S A -2.3505
82 R A -3.2258
83 V A 0.0000
84 E A -2.5628
85 A A -1.8243
86 E A -2.5559
87 D A 0.0000
88 V A -1.2018
89 G A 0.0000
90 V A -0.1787
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 0.2953
97 S A 0.0000
98 H A 0.2260
99 V A 1.5025
100 P A 0.7031
101 F A 0.7218
102 T A 0.4031
103 F A 0.3646
104 G A 0.0000
105 S A -0.0533
106 G A 0.0000
107 T A 0.0000
108 K A -0.7574
109 L A 0.0000
110 E A -1.8603
111 I A -1.8664
112 K A -2.3024
113 G A -1.7198
114 G A -1.6461
115 G A -1.4181
116 G A -1.6819
117 S A -1.2641
118 G A -1.5705
119 G A -1.6366
120 G A -1.7106
121 G A -1.7748
122 S A -1.0697
123 G A -1.4243
124 G A -1.3266
125 G A -1.2031
126 G A -1.0513
127 S A -0.8805
128 V A -0.8025
129 Q A -1.5187
130 L A 0.0000
131 V A -0.5402
132 Q A 0.0000
133 S A -0.7951
134 G A -0.7181
135 A A -0.0944
136 E A -0.2549
137 V A 0.8080
138 K A -1.0286
139 K A -2.2154
140 P A -2.3087
141 G A -1.6249
142 A A -1.2732
143 S A -1.3968
144 V A 0.0000
145 K A -2.0990
146 V A 0.0000
147 S A -0.8209
148 C A 0.0000
149 K A -1.3642
150 A A 0.0000
151 S A -0.8701
152 G A -0.7729
153 Y A -0.5188
154 T A -0.5970
155 F A 0.0000
156 T A -0.1373
157 D A -1.4255
158 Y A -0.6800
159 I A 0.1236
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 R A -0.4052
165 Q A -0.6607
166 A A -1.0479
167 P A -1.0435
168 G A -1.2115
169 Q A -1.6962
170 G A -0.9893
171 L A 0.0000
172 E A -0.5535
173 W A 0.0000
174 M A 0.0000
175 G A 0.0000
176 N A -0.2695
177 I A 0.0000
178 D A 0.1720
179 P A 0.0000
180 Y A 1.4143
181 Y A 1.7264
182 G A 0.4774
183 S A 0.2211
184 T A -0.1137
185 G A 0.0104
186 Y A -0.0799
187 A A 0.0000
188 L A 0.0328
189 K A -1.5395
190 F A 0.0000
191 K A -1.9577
192 G A -1.5145
193 R A -1.4394
194 V A 0.0000
195 T A -0.9242
196 M A 0.0000
197 T A -0.6586
198 R A -0.9129
199 D A -1.2650
200 T A -0.5298
201 S A -0.5771
202 T A -0.7146
203 S A -0.8233
204 T A 0.0000
205 V A 0.0000
206 Y A -0.8684
207 M A 0.0000
208 E A -1.5431
209 L A 0.0000
210 S A -1.1761
211 S A -1.2622
212 L A 0.0000
213 R A -3.1532
214 S A -2.4276
215 E A -2.5918
216 D A 0.0000
217 T A -0.9603
218 A A 0.0000
219 V A 0.1510
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 -0.9985
226 G A -0.9334
227 N A -1.1029
228 Y A -0.0547
229 G A 0.0000
230 S A 0.0000
231 D A -0.4290
232 Y A -0.5373
233 W A -0.5600
234 G A 0.0000
235 Q A -1.4677
236 G A -0.6878
237 T A 0.0000
238 T A -0.0251
239 V A 0.0000
240 T A -0.3814
241 V A 0.0000
242 S A -1.1349
243 S A -1.0372
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 -0.5729 1.9476 View CSV PDB
4.5 -0.6074 1.8582 View CSV PDB
5.0 -0.6477 1.7515 View CSV PDB
5.5 -0.6855 1.6376 View CSV PDB
6.0 -0.712 1.6117 View CSV PDB
6.5 -0.7215 1.5932 View CSV PDB
7.0 -0.7149 1.5749 View CSV PDB
7.5 -0.6975 1.5572 View CSV PDB
8.0 -0.6741 1.5407 View CSV PDB
8.5 -0.6461 1.5265 View CSV PDB
9.0 -0.6132 1.5345 View CSV PDB