Proteome Predictions

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Proteome Analysis

This module allows you to use a PoPS specificity model to search an entire proteome for possible targets.

Is you favourite organism missing from this page? Send an email request to Sarah Boyd (Sarah.Boyd@Infotech.monash.edu.au).
Alternatively, check out the proteome analysis from a fasta file, which allows you to do a proteome search from a fasta file.

Please note that results are only available for 72 hours

Select your settings here:

Please provide your email address (where the results will be sent):

Please provide the file name of the protease specificity model:

Select the organism (proteome):
Homo sapiens (human):    27,975 proteins^¶
Saccharomyces cerevisiae (baker's yeast):    5,876 proteins^¶
Escherichia coli K12:    4,242 proteins^¶
Drosophila melanogaster (fruit fly):    19,954 proteins^¶
Arabidopsis thaliana (thale cress):    29,157 proteins^¶
Rattus norvegicus (Norway rat):    22,849 proteins^¶
Mus musculus (house mouse):    26,549 proteins^¶
Danio rerio (zebrafish):    4,419 proteins^¶
Plasmodium falciparum (malaria):    5270 proteins^¶
Human herpesvirus 8:    869 proteins (Swiss-Prot: 4, TrEMBL: 865)^§
Schistosoma mansoni (Blood fluke):    410 proteins (Swiss-Prot: 81, TrEMBL: 329)^§

^¶Derived from the RefSeq database (NCBI): last updated on the 1st August 2004.
^§Derived from SwissProt and TrEMBL databases: last updated on the 14th September 2004.

Select the preferred threshold option:
Note that reasoning tables are limited to the top 10 sites in each protein, regardless of the threshold. See here for more details.
Set the threshold value (any valid floating point number)
Set the threshold to the maximum score in each protein (substrate)
Set the threshold to the minimum score (all predictions in each substrate except -Infinity)

Additional Options
(Click here to skip additional options and go to prediction submission).

Limit the output according to predicted accessibility:
In the proteome predictions, the accessibility is set to minimum 33% solvent accessible. Only the five most closely related structures are used.

Exclude predictions that have at least residue(s) predicted as buried in at least of the structures returned.

       treat residues of unknown accessibility as accessible.

       treat unknown structures as accessible.

Limit the output according to secondary structure:
Only the five most closely related structures are used. See below for the DSSP code.

Only return predictions that have at least:

residue(s) predicted as unstructured in at least structure(s):

       treat residues of unknown structure as unstructured.

       treat unknown structures as unstructured.

Exclude predictions that have at least:

residue(s) predicted as G in at least structure(s).

residue(s) predicted as H in at least structure(s).

residue(s) predicted as I in at least structure(s).

residue(s) predicted as T in at least structure(s).

residue(s) predicted as E in at least structure(s).

residue(s) predicted asc B in at least structure(s).

residue(s) predicted as S in at least structure(s).

residue(s) predicted as ? in at least structure(s).

For each of these selections:

remove the prediction if the number of specified structures is not available.

Limit the output according to the number of predicted sites:
Use the following options to exclude proteins from the results that have more than a specific number of predicted cleavage sites:
No Limit (default)
Exclude substrates containing more than predicted cleavage sites.



The DSSP code:

G = 3-turn helix (3_10 helix). Minimum length 3 residues.

H = 4-turn helix (alpha helix). Minimum length 4 residues.

I = 5-turn helix (pi helix). Minimum length 5 residues.

T = hydrogen bonded turn (3, 4 or 5 turn)

E = beta sheet in parallel and/or anti-parallel sheet conformation (extended strand). Minimum length 2 residues.

B = residue in isolated beta-bridge (single pair beta-sheet hydrogen bond formation)

S = bend (the only non-hydrogen-bond based assignment)

In addition, PoPS uses the symbol '?' to represent residues where the structure doesn't align, and blank spaces (' ') to represent where no structure was available.

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Only return predictions that have at least:
residue(s) predicted as unstructured in at least	structure(s):
treat residues of unknown structure as unstructured.
treat unknown structures as unstructured.

Exclude predictions that have at least:
residue(s) predicted as G in at least	structure(s).
residue(s) predicted as H in at least	structure(s).
residue(s) predicted as I in at least	structure(s).
residue(s) predicted as T in at least	structure(s).
residue(s) predicted as E in at least	structure(s).
residue(s) predicted asc B in at least	structure(s).
residue(s) predicted as S in at least	structure(s).
residue(s) predicted as ? in at least	structure(s).
For each of these selections:
remove the prediction if the number of specified structures is not available.