PDISORDER: A new Program for Finding Intrinsic Distorder Regions

Dan dmb at mrc-dunn.cam.ac.uk
Tue Aug 5 11:29:19 EST 2003


Does order mean 'structure'?

Do you have a paper?

Cheers,
Dan.

softberry at softberry.com wrote:
> PDISORDER: The 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: 
> 
> http://www.softberry.com/berry.phtml?
> topic=pdisorder&group=programs&subgroup=propt   or
> 
>  from Protein Structure Submeny at www.softberry.com
>  
> 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.
> 
>>gi|1352677|sp|P48457|P2B_EMENI Ser/thr protein phosphatase 2B catalytic 
> 
>     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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