Project name: 4AJY_S80R [mutate: SR80V]

Status: done

Started: 2020-09-18 14:32:22
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues SR80V
Energy difference between WT (input) and mutated protein (by FoldX) 18.4416 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
Downloads Download all the data
Simulation log 
[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 V chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:01:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:02:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:55)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:29:03)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:29:04)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:29:05)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:29:06)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:29:06)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:29:07)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:29:08)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:29:08)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:29:09)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:29:10)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:29:11)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:29:12)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:29:12)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:29:14)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:29:15)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:29:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:16)
Show buried residues
Minimal score value
-4.0723
Maximal score value
1.8627
Average score
-0.7168
Total score value
-106.0848
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
60 R V -1.5132
61 P V -1.3308
62 V V 0.0000
63 L V 0.8852
64 R V -0.0475
65 S V 0.6935
66 V V 0.8992
67 N V -0.9475
68 S V -1.3642
69 R V -2.5602
70 E V -2.1935
71 P V -2.0007
72 S V 0.0000
73 Q V -0.9849
74 V V 0.0000
75 I V 0.6549
76 F V 0.0000
77 C V -0.3664
78 N V 0.0000
79 R V -2.7043
80 R V -2.1591 mutated: SR80V
81 P V -1.8200
82 R V -2.2861
83 V V -1.0909
84 V V 0.0000
85 L V 0.0000
86 P V 0.0000
87 V V 0.0000
88 W V -0.0422
89 L V 0.0000
90 N V -0.2677
91 F V 0.0274
92 D V -1.8164
93 G V -1.5965
94 E V -1.2163
95 P V -0.8555
96 Q V -0.6251
97 P V -0.3855
98 Y V -0.1222
99 P V -0.2470
100 T V -0.2252
101 L V -0.6177
102 P V -1.1771
103 P V -1.3435
104 G V -1.6001
105 T V -1.0799
106 G V -0.9567
107 R V -1.4301
108 R V -1.8245
109 I V 0.0000
110 H V -1.6119
111 S V 0.0000
112 Y V 0.0000
113 R V -1.6770
114 G V -0.1776
115 H V 0.0000
116 L V 0.0000
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V -0.6654
121 D V 0.0000
122 A V -0.7291
123 G V -0.6190
124 T V -0.5604
125 H V -0.9645
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V 0.3300
130 V V 0.0000
131 N V -1.1429
132 Q V -1.4519
133 T V -0.5528
134 E V 0.0000
135 L V 0.0000
136 F V 0.0000
137 V V 0.7283
138 P V 0.0000
139 S V 0.2565
140 L V 0.9642
141 N V -0.4805
142 V V 0.5799
143 D V -1.6885
144 G V -1.1182
145 Q V 0.0000
146 P V 0.2908
147 I V 1.3365
148 F V 1.8627
149 A V 0.0000
150 N V -0.7248
151 I V 0.0000
152 T V -0.9697
153 L V 0.0000
154 P V 0.0951
155 V V 1.6416
156 Y V 1.7790
157 T V 1.0173
158 L V 1.3536
159 K V 0.2189
160 E V 0.1142
161 R V 0.0986
162 C V 0.8322
163 L V 0.0000
164 Q V 0.0000
165 V V 1.4686
166 V V 1.1691
167 R V -0.0925
168 S V 0.6863
169 L V 1.6065
170 V V 0.0062
171 K V -1.8584
172 P V -2.6675
173 E V -3.1692
174 N V -2.3994
175 Y V -2.3307
176 R V -4.0723
177 R V -3.3021
178 L V -1.7351
179 D V -2.1575
180 I V -0.1946
181 V V 0.3479
182 R V -1.7899
183 S V -1.3287
184 L V 0.0000
185 Y V -2.1483
186 E V -3.0015
187 D V -2.3429
188 L V -2.2812
189 E V -3.4250
190 D V -3.0445
191 H V -2.5758
192 P V -2.1812
193 N V -2.2954
194 V V -1.5584
195 Q V -2.3267
196 K V -2.5609
197 D V 0.0000
198 L V 0.0000
199 E V -3.3837
200 R V -2.9471
201 L V -2.0239
202 T V 0.0000
203 Q V -2.6447
204 E V -2.8812
205 R V -1.7130
206 I V 0.3686
207 A V -0.0316
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View in 3Dmol
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D 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 A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.7168 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 A3D Score
model_8 -0.7168 View CSV PDB
model_2 -0.7809 View CSV PDB
model_0 -0.8025 View CSV PDB
input -0.8096 View CSV PDB
model_6 -0.8419 View CSV PDB
model_4 -0.8501 View CSV PDB
model_7 -0.8772 View CSV PDB
model_11 -0.8886 View CSV PDB
model_9 -0.9741 View CSV PDB
model_5 -0.9822 View CSV PDB
model_1 -1.0457 View CSV PDB
model_10 -1.0753 View CSV PDB
model_3 -1.1152 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018