Project name: 5B5 MUTANT ANTIBODY 2

Status: done

Started: 2026-03-17 05:29:52
Chain sequence(s) A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGNTYLEWYLQKPGQPPQLLIYKLSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSQVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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                                          (00:01:54)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5e32b8f825d5fe9/tmp/folded.pdb                (00:01:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:12)
Show buried residues
Minimal score value
-3.129
Maximal score value
1.678
Average score
-0.628
Total score value
-152.5961
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 -1.1191
2 I A 0.0000
3 V A 0.7615
4 M A 0.0000
5 T A -0.2735
6 Q A 0.0000
7 T A 0.0460
8 P A 0.4657
9 L A 1.2670
10 S A 0.1578
11 L A -0.2248
12 S A -1.1210
13 V A 0.0000
14 T A -1.5939
15 P A -1.7320
16 G A -1.6074
17 Q A -1.8217
18 P A -1.9711
19 A A 0.0000
20 S A -0.8789
21 I A 0.0000
22 S A -0.8707
23 C A 0.0000
24 R A -2.2436
25 S A 0.0000
26 S A -1.0108
27 Q A -1.5843
28 S A -0.9037
29 L A 0.0000
30 V A 0.5637
31 H A -0.5198
32 S A -0.8414
33 N A -1.5584
34 G A -0.9576
35 N A -0.7583
36 T A -0.1954
37 Y A -0.0752
38 L A 0.0000
39 E A -0.3453
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A -0.8084
44 K A -1.4214
45 P A -1.0080
46 G A -1.3410
47 Q A -1.8002
48 P A -1.1317
49 P A 0.0000
50 Q A -0.8669
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A -0.6046
55 K A -1.0469
56 L A -0.7945
57 S A -0.9840
58 N A -1.2550
59 R A -1.6186
60 F A -0.5817
61 S A -0.5079
62 G A -0.9300
63 V A -0.8853
64 P A -1.2494
65 D A -2.4031
66 R A -2.2978
67 F A 0.0000
68 S A -1.5364
69 G A 0.0000
70 S A -1.0233
71 G A -1.0304
72 S A -0.6749
73 G A -0.6091
74 T A -1.4158
75 D A -2.0799
76 F A 0.0000
77 T A -1.1467
78 L A 0.0000
79 K A -2.1981
80 I A 0.0000
81 S A -2.3397
82 R A -3.1290
83 V A 0.0000
84 E A -2.1664
85 A A -1.6782
86 E A -2.2068
87 D A 0.0000
88 V A -0.8619
89 G A 0.0000
90 V A -0.0274
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 0.0429
97 S A 0.0000
98 Q A -0.3777
99 V A 1.1723
100 P A 0.4983
101 F A 0.5348
102 T A 0.3320
103 F A 0.3437
104 G A 0.0000
105 S A -0.0223
106 G A 0.0000
107 T A 0.0000
108 K A -0.4381
109 L A 0.0000
110 E A -1.6273
111 I A -1.8269
112 K A -2.3688
113 G A -1.8315
114 G A -1.8097
115 G A -1.3543
116 G A -1.3386
117 S A -1.2222
118 G A -1.6839
119 G A -1.4980
120 G A -1.8025
121 G A -1.4350
122 S A -1.1956
123 G A -1.2588
124 G A -1.2986
125 G A -1.2500
126 G A -1.0544
127 S A -0.8987
128 V A -0.8578
129 Q A -1.3320
130 L A 0.0000
131 V A 0.2314
132 Q A 0.0000
133 S A -0.5930
134 G A -0.6494
135 A A -0.1186
136 E A -0.2669
137 V A 0.8093
138 K A -0.9642
139 K A -2.1332
140 P A -2.1531
141 G A -1.4950
142 A A -1.1859
143 S A -1.2876
144 V A 0.0000
145 K A -1.9285
146 V A 0.0000
147 S A -0.6275
148 C A 0.0000
149 K A -0.8899
150 A A 0.0000
151 S A -0.6799
152 G A -0.7677
153 Y A -0.4957
154 T A -0.5786
155 F A 0.0000
156 T A -0.1478
157 D A -1.4188
158 Y A -0.6795
159 I A 0.0761
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 R A -0.4304
165 Q A -0.6865
166 A A -1.0629
167 P A -1.0502
168 G A -1.2153
169 Q A -1.7063
170 G A -0.9894
171 L A 0.0000
172 E A -0.5819
173 W A 0.0000
174 M A 0.0000
175 G A 0.0000
176 N A -0.1266
177 I A 0.0000
178 D A 0.0980
179 P A 0.0000
180 Y A 1.3734
181 Y A 1.6780
182 G A 0.3831
183 S A 0.2025
184 T A -0.1374
185 G A 0.0014
186 Y A -0.0753
187 A A 0.0000
188 L A 0.0554
189 K A -1.5368
190 F A 0.0000
191 K A -1.9602
192 G A -1.4962
193 R A -1.4013
194 V A 0.0000
195 T A -0.9070
196 M A 0.0000
197 T A -0.7434
198 R A -1.0646
199 D A -1.2893
200 T A -0.5706
201 S A -0.5885
202 T A -0.6832
203 S A -0.7688
204 T A 0.0000
205 V A 0.0000
206 Y A -0.8338
207 M A 0.0000
208 E A -1.4703
209 L A 0.0000
210 S A -1.0592
211 S A -1.0831
212 L A 0.0000
213 R A -2.7957
214 S A -2.2632
215 E A -2.4821
216 D A 0.0000
217 T A -0.8912
218 A A 0.0000
219 V A 0.1217
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 -1.1353
226 G A -0.9876
227 N A -1.0975
228 Y A -0.4220
229 G A 0.0000
230 S A 0.0000
231 D A -0.4060
232 Y A -0.4070
233 W A -0.4205
234 G A 0.0000
235 Q A -1.2554
236 G A -0.5630
237 T A 0.0000
238 T A -0.0486
239 V A 0.0000
240 T A -0.3411
241 V A 0.0000
242 S A -1.0739
243 S A -0.9917
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 -0.5999 1.9964 View CSV PDB
4.5 -0.6304 1.9648 View CSV PDB
5.0 -0.6664 1.9156 View CSV PDB
5.5 -0.7005 1.8395 View CSV PDB
6.0 -0.7246 1.7386 View CSV PDB
6.5 -0.733 1.6238 View CSV PDB
7.0 -0.7259 1.5318 View CSV PDB
7.5 -0.7083 1.5374 View CSV PDB
8.0 -0.6848 1.6068 View CSV PDB
8.5 -0.6567 1.6754 View CSV PDB
9.0 -0.6241 1.7413 View CSV PDB