Project name: 1LM8_WT3

Status: done

Started: 2020-09-20 09:16:30
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQ
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
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]       CABS:     Running CABS flex simulation                                                (00:01:41)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:27)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:28)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:20:29)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:29)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:30)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:31)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:31)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:32)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:33)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:33)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:20:34)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:35)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:35)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:20:37)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:37)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:20:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:20:38)
Show buried residues
Minimal score value
-4.385
Maximal score value
2.2406
Average score
-0.7905
Total score value
-118.5762
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 -1.8878
61 P V -0.6128
62 V V 0.9008
63 L V 0.2789
64 R V 0.4019
65 S V 1.2271
66 V V 1.7507
67 N V -0.2464
68 S V -1.3482
69 R V -2.8597
70 E V -2.2261
71 P V -1.9160
72 S V 0.0000
73 Q V -1.1181
74 V V 0.0000
75 I V 0.4672
76 F V 0.0000
77 C V -0.5532
78 N V 0.0000
79 R V -2.3681
80 S V -1.4541
81 P V 0.0000
82 R V -1.8303
83 V V -0.4687
84 V V 0.0000
85 L V 0.0641
86 P V 0.0000
87 V V 0.0000
88 W V -0.0499
89 L V 0.0000
90 N V 0.0000
91 F V 0.9905
92 D V -1.2120
93 G V -0.9646
94 E V -1.1100
95 P V -0.7335
96 Q V -0.7672
97 P V -0.4105
98 Y V -0.2136
99 P V -0.0719
100 T V 0.0010
101 L V 0.0000
102 P V -0.9411
103 P V -1.4829
104 G V -1.4761
105 T V -1.1339
106 G V -1.2028
107 R V -1.3630
108 R V -1.9830
109 I V 0.0000
110 H V -1.6940
111 S V 0.0000
112 Y V 0.0000
113 R V -1.8697
114 G V -0.3486
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 -0.1983
121 D V 0.0000
122 A V -0.5015
123 G V -0.1906
124 T V 0.3356
125 H V -0.4007
126 D V 0.0000
127 G V 0.0000
128 L V -0.0121
129 L V -0.0866
130 V V -0.8963
131 N V -1.5436
132 Q V -1.6549
133 T V -1.0692
134 E V -1.5904
135 L V 0.0000
136 F V 0.0000
137 V V 0.6751
138 P V 0.0000
139 S V -0.2532
140 L V -0.0153
141 N V -1.7170
142 V V -1.5926
143 D V -2.4886
144 G V -2.0847
145 Q V -1.5072
146 P V -0.3592
147 I V 0.9169
148 F V 1.8473
149 A V 0.0000
150 N V -0.7376
151 I V 0.0000
152 T V -0.6454
153 L V 0.0000
154 P V 0.0000
155 V V 0.5450
156 Y V 1.3630
157 T V 0.5075
158 L V 0.6601
159 K V -0.8684
160 E V -0.4667
161 R V 0.1584
162 C V 0.8458
163 L V 0.8452
164 Q V 0.0000
165 V V 2.2406
166 V V 1.8752
167 R V 0.0000
168 S V 0.8969
169 L V 1.7889
170 V V -0.2047
171 K V -2.2125
172 P V -2.4867
173 E V -3.3449
174 N V -2.7002
175 Y V 0.0000
176 R V -3.8412
177 R V -3.1428
178 L V -1.2444
179 D V -1.7003
180 I V 0.2592
181 V V 0.6768
182 R V -1.8065
183 S V -1.2806
184 L V -0.8353
185 Y V -1.9235
186 E V -3.0309
187 D V -2.8831
188 L V 0.0000
189 E V -2.8908
190 D V -3.2194
191 H V -2.5061
192 P V -2.4886
193 N V -2.7378
194 V V -1.9280
195 Q V -2.9588
196 K V -3.7515
197 D V 0.0000
198 L V 0.0000
199 E V -4.3850
200 R V -4.2116
201 L V 0.0000
202 T V -2.8014
203 Q V -3.3401
204 E V -3.6268
205 R V -2.8797
206 I V -0.5890
207 A V -1.4054
208 H V -2.1714
209 Q V -1.7690
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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, -0.7905 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_0 -0.7905 View CSV PDB
model_6 -0.8384 View CSV PDB
model_8 -0.8725 View CSV PDB
model_9 -0.8767 View CSV PDB
model_5 -0.9164 View CSV PDB
model_3 -0.9356 View CSV PDB
model_4 -0.9503 View CSV PDB
model_1 -0.9535 View CSV PDB
model_7 -0.9627 View CSV PDB
input -0.9762 View CSV PDB
model_2 -0.9889 View CSV PDB
model_11 -0.9961 View CSV PDB
model_10 -1.0157 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018