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PDISORDER: A new Program for Finding Intrinsic Distorder Regions in Protein Sequences

PDISORDER: A new Program for Finding Intrinsic Distorder Regions in Protein Sequences - Protein Forum

PDISORDER: A new Program for Finding Intrinsic Distorder Regions in Protein Sequences - Protein Forum


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Old 07-30-2003, 11:29 PM
softberry@softberry.com
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Default PDISORDER: A new Program for Finding Intrinsic Distorder Regions in Protein Sequences



PDISORDER: A new Program for Finding Intrinsic Distorder Regions in Protein
Sequences

PDISORDER V. 1.0 is the program for predicting ordered and disordered regions
in
protein sequences. Minimum required sequence length is 40. The algorithm is
based on
three-layered neural net with 10 neurons in each layer.

You can run program at:

[Only registered users see links. ]
topic=pdisorder&group=programs&subgroup=propt

or from Protein Structure Sub-menu at [Only registered users see links. ]

It is increasingly evident that intrinsically unstructured protein regions
play
key roles in cell-signaling, regulation and cancer
(Iakoucheva et al., J. Mol. Biol. (2002) 323, 573-584),
which makes them extremely useful for discovery of anticancer drugs.
Requrement of intrinsic structural distorder is shown for many protein
functions - see,
for instance, Dunker et al., Biochemistry (2002) 41 (21), 6573 -6582.

Example of PDISORDER output:

Prediction of disordered regions in proteins. Softberry Inc.
subunitCalmodulin-dependent calcineurin A subunit)
10 20 30 40
Pred_od ooooooooo ddd ooooooooooooooooooooooooooooooooo
AA seq MEDGTQVSTLERVVKEVQAPALNKPSDDQFWDPEEPTKPNLQFLKQHFYR
Prob_o 66666665655663335777766565589767999999999999997999
60 70 80 90
Pred_od oooooooooooooooooooooooooooooooooooooooooooooooooo
AA seq EGRLTEDQALWIIQAGTQILKSEPNLLEMDAPITVCGDVHGQYYDLMKLF
Prob_o 99999999999999999999999999999999999999999999999999
110 120 130 140
Pred_od oooooooooooooooooooooooooooooooooooooooooooooooooo
AA seq EVGGDPAETRYLFLGDYVDRGYFSIECVLYLWALKIWYPNTLWLLRGNHE
Prob_o 99999999999999999999999999999999999999999999999999
160 170 180 190
Pred_od oooooooooooooooooooooooooooooooooooooooooooooooooo
AA seq CRHLTDYFTFKLECKHKYSERIYEACIESFCALPLAAVMNKQFLCIHGGL
Prob_o 99999999999999999999999999999999999997555556887888
210 220 230 240
Pred_od oooooooooooooooooooooooooooooooooooooooooooooooooo
AA seq SPELHTLEDIKSIDRFREPPTHGLMCDILWADPLEDFGQEKTGDYFIHNS
Prob_o 78775555553563478776666666678689999999999999999999
260 270 280 290
Pred_od oooooooooooooooooooooooooooooooooooooooooooooooooo
AA seq VRGCSYFFSYPAACAFLEKNNLLSVIRAHEAQDAGYRMYRKTRTTGFPSV
Prob_o 99999999999999999999999999999999999999999999999999
310 320 330 340
Pred_od oooooooooooooooooooooooooooooooooooooooooooooooooo
AA seq MTIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCTPHPYWLPNFMDVFTW
Prob_o 99999999999999999999999999999999999999999999999999
360 370 380 390
Pred_od ooooooooooo dddddddddddddddddddddddddddd
AA seq SLPFVGEKITDIVIAILNTCSKEELEDETPSTISPAEPSPPMPMDTVDTE
Prob_o 99999976656555554444441100000000000000000000000000
410 420 430 440
Pred_od dddddddddddddddddddddddddddddddddddddddddddddddddd
AA seq STEFKRRAIKNKILAIGRLSRVFQVLREESERVTELKTAAGGRLPAGTLM
Prob_o 00000000000100000000001223333444444333422232555555
460 470 480 490
Pred_od dddddddddddddddddddddddddddddddddddddddddddddddddd
AA seq LGAEGIKQAITNFEDARKVDLQNERLPPSHDEVVRRSEEERRIALDRAQH
Prob_o 55555433255544555565443400000231112100000000000001
510 520
Pred_od dddddddddddddddddddddddddddddd
AA seq EADNDTGLATVARRISMVRRIRKIPSTTRR
Prob_o 020000022332232444444444443343


sequences=1 disordered=161 ordered=353 unknown=16


Here line Pred_od shows ordered (o) and disordered (d) regions. Blanks denote
undefined-state stretches, usually at the boundaries of disordered reqions.

Line Prob_o shows raw probability on a scale of 0 to 9 for each aminoacid
residue to be in ordered region.

The line at the end of the output shows total number of sequence residues i
n each state: disordered, ordered and unknown.

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