Project name: 5B5 MUTANT ANTIBODY 13

Status: done

Started: 2026-03-17 05:36:56
Chain sequence(s) A: DIVMTQTPLSLPVTPGEPASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYNLKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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                                          (00:00:13)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:16)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/844b400b6f14ece/tmp/folded.pdb                (00:03:16)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:18)
Show buried residues
Minimal score value
-3.5519
Maximal score value
1.7154
Average score
-0.6199
Total score value
-150.634
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 -1.0405
2 I A 0.0000
3 V A 0.7594
4 M A 0.0000
5 T A -0.2817
6 Q A 0.0000
7 T A 0.0204
8 P A 0.4375
9 L A 1.2232
10 S A 0.0552
11 L A -0.3396
12 P A -1.2831
13 V A 0.0000
14 T A -1.9160
15 P A -2.2245
16 G A -2.1604
17 E A -2.8774
18 P A -2.5170
19 A A 0.0000
20 S A -0.9147
21 I A 0.0000
22 S A -0.8918
23 C A 0.0000
24 R A -2.2774
25 S A 0.0000
26 S A -0.9824
27 Q A -1.5392
28 S A -1.0190
29 I A 0.0000
30 V A -0.0442
31 H A -0.7638
32 S A -1.0010
33 N A -1.6641
34 G A -1.1312
35 N A -0.8164
36 T A -0.2855
37 Y A 0.0677
38 L A 0.0000
39 E A -0.1401
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A -0.8870
44 K A -1.5805
45 P A -1.1989
46 G A -1.5314
47 Q A -2.1313
48 S A -1.2898
49 P A 0.0000
50 Q A -0.9802
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A 0.0876
55 K A -0.2457
56 L A -0.1214
57 S A -0.0501
58 Y A 0.5868
59 R A -0.9789
60 A A 0.0000
61 S A -0.3727
62 G A -1.1419
63 V A 0.0000
64 P A -1.4481
65 D A -2.5307
66 R A -2.3418
67 F A 0.0000
68 S A -1.3885
69 G A -0.7673
70 S A -0.7856
71 G A -1.0194
72 S A -0.7754
73 G A -0.8063
74 T A -1.5025
75 D A -2.0821
76 F A 0.0000
77 T A -1.1833
78 L A 0.0000
79 K A -2.2746
80 I A 0.0000
81 S A -2.6023
82 R A -3.5519
83 V A 0.0000
84 E A -2.5266
85 A A -1.6474
86 E A -2.1859
87 D A 0.0000
88 V A -1.0270
89 G A 0.0000
90 V A -0.1094
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 0.3452
97 S A 0.0000
98 H A 0.2356
99 V A 1.5080
100 P A 0.0000
101 F A 0.7239
102 T A 0.4030
103 F A 0.3447
104 G A 0.0000
105 S A -0.0168
106 G A 0.0000
107 T A 0.0000
108 K A -0.5900
109 L A 0.0000
110 E A -1.9495
111 I A -1.9176
112 K A -2.4144
113 G A -1.8276
114 G A -1.7387
115 G A -1.4824
116 G A -1.2789
117 S A -1.2310
118 G A -1.5262
119 G A -1.6386
120 G A -1.7242
121 G A -1.7371
122 S A -1.0881
123 G A -1.3413
124 G A -1.2742
125 G A -1.2108
126 G A -1.0980
127 S A -0.8896
128 V A -0.7063
129 Q A -1.1962
130 L A 0.0000
131 V A 0.0182
132 Q A 0.0000
133 S A -0.6338
134 G A -0.6761
135 A A -0.1228
136 E A -0.2252
137 V A 0.8507
138 K A -0.8383
139 K A -2.0428
140 P A -2.0424
141 G A -1.3811
142 A A -1.1181
143 S A -1.2234
144 V A 0.0000
145 K A -1.7625
146 V A 0.0000
147 S A -0.6502
148 C A 0.0000
149 K A -1.0414
150 A A 0.0000
151 S A -0.6655
152 G A -0.7266
153 Y A -0.4739
154 T A -0.4481
155 F A 0.0000
156 T A -0.1485
157 D A -1.5673
158 Y A -0.7344
159 I A -0.0449
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 R A -0.4291
165 Q A -0.6834
166 A A -1.0465
167 P A -1.0409
168 G A -1.2167
169 Q A -1.7057
170 G A -0.9963
171 L A 0.0000
172 E A -0.5334
173 W A 0.0000
174 M A 0.0000
175 G A 0.0000
176 N A -0.2516
177 I A 0.0000
178 D A 0.1394
179 P A 0.0000
180 Y A 1.3743
181 Y A 1.7154
182 G A 0.4533
183 S A 0.1957
184 T A -0.0655
185 G A 0.2551
186 Y A 0.1131
187 N A 0.0000
188 L A 0.0878
189 K A -1.5227
190 F A 0.0000
191 K A -1.9102
192 G A -1.4810
193 R A -1.3887
194 V A 0.0000
195 T A -0.8391
196 M A 0.0000
197 T A -0.7519
198 R A -1.1637
199 D A -1.2968
200 T A -0.5744
201 S A -0.5941
202 T A -0.7134
203 S A -0.8106
204 T A 0.0000
205 V A 0.0000
206 Y A -0.8025
207 M A 0.0000
208 E A -1.3736
209 L A 0.0000
210 S A -1.0375
211 S A -1.0891
212 L A 0.0000
213 R A -2.6748
214 S A -2.1842
215 E A -2.4498
216 D A 0.0000
217 T A -0.8595
218 A A 0.0000
219 V A 0.1100
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 -1.0989
226 G A -0.7456
227 N A -0.9795
228 Y A 0.5552
229 G A 0.0000
230 S A -0.3277
231 D A 0.0000
232 Y A -0.2838
233 W A -0.4295
234 G A 0.0000
235 Q A -1.3482
236 G A -0.6382
237 T A 0.0000
238 T A -0.0551
239 V A 0.0000
240 T A -0.3023
241 V A 0.0000
242 S A -1.0260
243 S A -0.9572
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 -0.5713 1.9562 View CSV PDB
4.5 -0.6056 1.8651 View CSV PDB
5.0 -0.6477 1.7545 View CSV PDB
5.5 -0.6884 1.644 View CSV PDB
6.0 -0.7184 1.6243 View CSV PDB
6.5 -0.7318 1.6045 View CSV PDB
7.0 -0.7286 1.5849 View CSV PDB
7.5 -0.7135 1.566 View CSV PDB
8.0 -0.6916 1.5486 View CSV PDB
8.5 -0.6649 1.5339 View CSV PDB
9.0 -0.6334 1.5469 View CSV PDB