[BiO BB] atomic coordinates of the proteins to predict proteintertiary structure using adaptive neuro-fuzzy systems
Mike Marchywka
marchywka at hotmail.com
Wed Dec 27 13:52:51 EST 2006
If you really get stuck, this same problem comes up in just about all
related fields- machine vision
was dealing with a 2D problem in the 80's ( how do you get a translationally
and rotationally
tolerant measure-of-widgetness from a picture?). Image analysis and
recognition literature
may be heplful and, in any case, I think most of the stuff from all fields
is on citeseer:
http://citeseer.ist.psu.edu/
( note new address as of 10-06)
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165r
( NOTE MORE NEWER NUMBER )
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
>From: "soorya kiran" <kiran.soorya at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org"
><bio_bulletin_board at bioinformatics.org>
>To: bio_bulletin_board at bioinformatics.org
>Subject: [BiO BB] atomic coordinates of the proteins to predict
>proteintertiary structure using adaptive neuro-fuzzy systems
>Date: Mon, 25 Dec 2006 02:41:18 -0800
>
>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.
>_______________________________________________
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
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