[BiO BB] atomic coordinates of the proteins to predict protein tertiary structure using adaptive neuro-fuzzy systems
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:
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:
For 1YMB, the co-ordinates of the first few alpha carbon atoms are as
For 2MM1, the atomic co-ordinates of the first few atomic coordinates are as
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
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
Our understanding is there are many tools for aligning the alpha carbon
atoms of proteins, but they do not give the atomic coordinates after
Thanks and regards,
Srijith V. M.
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