Aggrescan3D: Savannah Mary Mather

Project name: Savannah Mary Mather

Status: done

Started: 2020-11-19 18:21:01

Settings

Chain sequence(s)	X: SFNPTQRLQKESPVKDSNKDSEKLQETMSSMSSGGATSTRKALKIEVERGS input PDB
Selected Chain(s)	X
Distance of aggregation	10 Å
FoldX usage	Yes
Dynamic mode	Yes
Automated mutations	No
Downloads	Download all the data

Simulation log

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[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)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with X chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:54)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:06:11)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:06:11)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:06:11)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:06:11)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:06:12)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:06:12)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:06:12)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:06:12)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:06:12)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:06:13)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:06:13)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:06:13)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:06:13)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:06:14)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:06:14)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:06:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:14)

Note Your prediction results will be deleted after 360 days.

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Show buried residues

Minimal score value: -2.5373
Maximal score value: 1.6765
Average score: -0.7281
Total score value: -37.1319

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
130	S	X	0.1698
131	F	X	1.2152
132	N	X	0.0000
133	P	X	-0.6097
134	T	X	-1.1969
135	Q	X	-1.4246
136	R	X	0.0000
137	L	X	0.2384
138	Q	X	-1.5543
139	K	X	-2.5373
140	E	X	-1.7395
141	S	X	-1.5506
142	P	X	-0.9490
143	V	X	-0.7090
144	K	X	-2.2010
145	D	X	0.0000
146	S	X	-2.0155
147	N	X	-1.9015
148	K	X	0.0000
149	D	X	-2.1160
150	S	X	-1.0475
151	E	X	0.0000
152	K	X	0.0451
153	L	X	1.1374
154	Q	X	-0.2984
155	E	X	-1.3107
156	T	X	-1.0805
157	M	X	-0.6755
158	S	X	-0.9821
159	S	X	-0.5325
160	M	X	0.3007
161	S	X	-0.1175
162	S	X	-0.4353
163	G	X	-0.7337
164	G	X	-0.8002
165	A	X	-0.3550
166	T	X	-0.2237
167	S	X	-0.6807
168	T	X	-1.1726
169	R	X	-2.4132
170	K	X	-2.4387
171	A	X	-0.9730
172	L	X	0.5816
173	K	X	0.0032
174	I	X	1.6765
175	E	X	0.0000
176	V	X	0.5914
177	E	X	-1.8698
178	R	X	-2.2034
179	G	X	-1.4384
180	S	X	-0.8039

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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, -0.7281 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_4	-0.7281	View	CSV	PDB
model_6	-0.9457	View	CSV	PDB
model_10	-1.0187	View	CSV	PDB
model_5	-1.0375	View	CSV	PDB
model_9	-1.1296	View	CSV	PDB
model_3	-1.2141	View	CSV	PDB
model_1	-1.229	View	CSV	PDB
model_11	-1.2652	View	CSV	PDB
model_2	-1.3079	View	CSV	PDB
model_0	-1.3751	View	CSV	PDB
model_7	-1.4092	View	CSV	PDB
input	-1.545	View	CSV	PDB
model_8	-1.6137	View	CSV	PDB

Project name: Savannah Mary Mather

Status: done

Started: 2020-11-19 18:21:01

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score