[BiO BB] atomic coordinates of the proteins to predict protein tertiary structure using adaptive neuro-fuzzy systems
soorya kiran
kiran.soorya at gmail.com
Mon Dec 25 05:41:18 EST 2006
Sub: atomic coordinates of the proteins to predict protein tertiary
structure using adaptive neuro-fuzzy systems
We are trying to predict protein tertiary structure using adaptive
neuro-fuzzy systems. This method comes in the category of homology modeling,
since we are using homologous proteins for prediction.
We are facing a few problems in deriving the training data.
As an example, consider a situation where I use 2 proteins (PDB Ids: 1MYJ
and 1YMB) to predict the structure of the protein 'Human Myoglobin' (PDB Id:
2MM1).
I am attaching the co-ordinates of the first alpha carbons herewith.
For 1MYJ, the first few alpha carbon have atomic co-ordinates as follows:
GLY
48.763
-12.39
28.42
LEU
52.541
-11.96
28.764
SER
54.79
-13.074
25.979
ASP
56.15
-16.567
25.988
GLY
59.289
-14.893
27.105
GLU
57.708
-13.153
30.06
TRP
56.174
-16.476
31.235
GLN
59.566
-17.977
31.117
For 1YMB, the co-ordinates of the first few alpha carbon atoms are as
follows:
GLY
-3.12
15.454
14.959
LEU
-0.482
14.622
17.641
SER
-1.126
13.415
21.177
ASP
0.851
14.53
24.209
GLY
2.401
11.015
24.161
GLU
3.737
11.867
20.724
TRP
4.724
15.486
21.478
GLN
6.75
14.065
24.424
For 2MM1, the atomic co-ordinates of the first few atomic coordinates are as
follows:
GLY
-4.704
17.705
14.942
LEU
-1.187
18.608
16.091
SER
-0.042
17.772
19.588
ASP
0.651
20.497
22.117
GLY
4.297
19.54
21.663
GLU
3.879
19.913
17.893
TRP
2.244
23.408
18.097
GLN
5.159
24.505
20.293
You can notice that even though the amino acids are the same, their atomic
co-ordinates are completely different. This is not because of the amino
acids which follows in the sequence, since all these 3 proteins have very
similar sequence.
I infer this is because, the atomic co-ordinates may not absolute and cannot
be taken as such for training. We faced this issue while using this data for
training neural networks, since neural networks won't know *which
co-ordinates* to predict.
Can you suggest any means by which we can get the atomic coordinates of the
proteins used for training, after alignment?
That means, all the proteins used for training, should be aligned first and
then, we need to get the co-ordinates so that we can use those data for
training.
Our understanding is there are many tools for aligning the alpha carbon
atoms of proteins, but they do not give the atomic coordinates after
alignment."
Thanks and regards,
Srijith V. M.
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