PepSite

A structural method to predict peptide/protein binding
Evangelia Petsalaki, Alexander Stark, Eduardo Garcia Urdiales, Rob Russell

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If you have any problems or questions regarding PepSite please do not hesitate to contact us.


Example Ago

The id of your job is: 483a96e81c14.

The title of your job is Example_Ago
Your input peptide is PDNGTSAWGE
Your identifier is 1w9h
The chain id you provided is A


1w9hA

Display: Select: Colours:
Show Predictions: Other options:
Color scheme shapely:
ARG Dark BlueHISLila
METTanGLNOrange red
LYSBlueSEROrange
VALPinkASNSalmon
ASPPink-redTHRDark orange
ILEForest greenGLYWhite
GLUBrownPHEGrey
LEUGrey greenALALight green
CYSLight yellowTYRDark salmon
PRODark GreyTRPBrown Green
PTRMagentaTPOMagenta
SEPMagentaOtherMagenta
Color scheme amino:
ARGBlueHISLight Blue
METYellowGLNCyan
LYSBlueSEROrange
VALGreenASNCyan
ASPRedTHROrange
ILEGreenGLYWhite-grey
GLURedPHEDark blue
LEUGreenALAGrey
CYSYellowTYRDark blue
PROPinkTRPPurple
PTRLight BrownTPOLight Brown
SEPLight BrownOtherLight Brown
Color scheme cpk:
CarbonLight greyOxygenRedNitrogenLight blueSulforYellow


Color scheme structure:
HelixMagentaB-sheetYellowLoopsWhite



RESULTS SUMMARY

The default setting shows the first 5 predicted peptide chains as spacefilled atoms. Each spacefilled atom in the jmol interface represents the center of mass of the active part of the corresponding peptide residue.

Confidence decreases as follows:
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PEPTIDE P-VALUE: This score represents the probability that a random match gets a score is equal or higher to this value.
RESIDUES P-VALUE: This score shows the average p-value for each individual residue prediction. This score is included as a supplement to the PEPTIDE P-VALUE for cases that are ambiguous or for short peptides (for more details please visit our help page)

In the initial peptide row the residues are colored by p-value, in the matched residue row they are colored shapely, to correspond to the jmol interface.

CHAIN 1:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 2:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 3:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 4:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 5:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 6:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 7:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 8:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0034860.000019

CHAIN 9:
initial peptide (colored by confidence)P-1D-2N-3G-4T-5S-6A-7W-8G-9E-10peptideresidues
matched residues (colored by residue type)P------T----W----p-value0.0051520.000019



The output comprises two files:
  1. The first file is the pdb file that contains:
    • The original structure,(chain id you provided)
    • The predictions for potential binding sites of each individual residue in your peptide (chain U)
    • The top 9 peptides that were predicted for binding (chains 1-9).

  2. The second file is the predictions of the peptides, where they bind and confidence values to evaluate this.This file contains certain columns as follows:
    • The first column is labeled 'Template' and shows which residues in your peptide sequence have been matched.
    • The second column is labeled 'Prediction' and shows the corresponding residues in chain U that have been matched with the residues in your peptide sequence.
    • The score represents the raw score for the prediction of the binding site of this peptide. It is an average of the scores of each matched residue.
    • The next column is labeled 'PEPTIDE P-VALUE' and is the probability that a random match would get this score. The lower the p-value the better the prediction. The predictions are colored in the results summary table with red as the most reliable and blue the least reliable prediction.
    • The next column is labeled 'RESIDUES P-VALUE' and is the average of the p-values for each of the matched residues. This value is useful for fotifying the conclusion about the peptide binding site prediction and in cases of short peptides. (For more details please visit our help page)

You can download the output pdb file here and the full list of predictions and their scores here
For more details and interpretations of the results please look here



For the visualization of the results we are using Jmol.