Proteome Predictions

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Proteome Analysis from a FASTA File

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

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:

Please provide the fasta file with the proteins to be analysed:

Select the preferred threshold option:
Set the threshold to the integer value
Set the threshold to the maximum score in each protein (substrate)

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.