Intelligent Computing Lab.
Bioinformatics in NCTU, Taiwan.
Home

POPI2.0: a web server for predicting immunogenicity of MHC class I and II binding peptides

Home | About | Download | Help | Developer || Release 2.1, Last update: Dec 11 2009 

POPI 2.0: a web server for predicting immunogenicity of binding peptides of MHC class I and II


Content:

What is the definition of immunogenicity of POPI

What are the informative physicochemical properties used to implement POPI

How to submit peptides for prediction

How to cite POPI


The definition of immunogenicity

The immunogenicity of MHC binding peptides is determined by measuring:

MHC class I ) the concentration of peptides giving 50% of maximum specific lysis by CTLs of target cells displaying the peptide.

MHC class II) the peptide concentration giving 50% of maximum T-cell proliferation induced by cell displaying the MHC class IIVpeptide complex

Table 1 shows the PD50 values of immunogenicity classes defined by MHCPEP, (Brusic et al., 1998).

Table 1. The immunigenicity classes and the corresponding PD50 values
PD50 Immunogenicity class
> 10 mM none
10 mM–100 nM little
100 nM–1 nM moderate
< 1 nM high

[Back to content]


The informative physicochemical properties used to implement POPI

1) The part of POPI for predicting immunogenicity of MHC class I binding peptides is implemented by using 23 informative physicochemical properties and SVM.

2) The part of POPI for predicting immunogenicity of MHC class II binding peptides is implemented by using 23 informative physicochemical properties and SVM.

Table 2 and 3 shows the 23 (MHC class I) and 21 (MHC class II) informative physicochemical properties selected by inheritable bi-objective genetic algorithm (IBCGA, Ho et al., 2004).

The ID and description of physicochemical properties are extracted from AAindex, Amino acid indices and similarity matrices (Kawashima and Kanehisa., 2000).

Table 2. The used 23 informative physicochemical properties (MHC class I).
AAindex ID Description
FAUJ880113 pK-a(RCOOH) (Fauchere et al., 1988)
GEIM800103 Alpha-helix indices for beta-proteins (Geisow-Roberts, 1980)
HUTJ700102 Absolute entropy (Hutchens, 1970)
ISOY800106 Normalized relative frequency of helix end (Isogai et al., 1980)
JOND750101 Hydrophobicity (Jones, 1975)
KARP850103 Flexibility parameter for two rigid neighbors (Karplus-Schulz, 1985)
MIYS850101 Effective partition energy (Miyazawa-Jernigan, 1985)
OOBM770104 Average non-bonded energy per residue (Oobatake-Ooi, 1977)
OOBM850102 Optimized propensity to form reverse turn (Oobatake et al., 1985)
PALJ810115 Normalized frequency of turn in alpha+beta class (Palau et al., 1981)
QIAN880112 Weights for alpha-helix at the window position of 5 (Qian-Sejnowski, 1988)
QIAN880114 Weights for beta-sheet at the window position of -6 (Qian-Sejnowski, 1988)
QIAN880124 Weights for beta-sheet at the window position of 4 (Qian-Sejnowski, 1988)
QIAN880125 Weights for beta-sheet at the window position of 5 (Qian-Sejnowski, 1988)
QIAN880132 Weights for coil at the window position of -1 (Qian-Sejnowski, 1988)
RACS820113 Value of theta(i) (Rackovsky-Scheraga, 1982)
RADA880106 Accessible surface area (Radzicka-Wolfenden, 1988)
WEBA780101 RF value in high salt chromatography (Weber-Lacey, 1978)
MUNV940101 Free energy in alpha-helical conformation (Munoz-Serrano, 1994)
NADH010106 Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001)
MITS020101 Amphiphilicity index (Mitaku et al., 2002)
GEOR030105 Linker propensity from small dataset (linker length is less than six residues) (George-Heringa, 2003)
DIGM050101 Hydrostatic pressure asymmetry index, PAI (Di Giulio, 2005)

Table 3. The used 21 informative physicochemical properties (MHC class II).
AAindex ID Description
BIOV880102 Information value for accessibility; average fraction 23% (Biou et al., 1988)
CHOC750101 Average volume of buried residue (Chothia, 1975)
DESM900102 Average membrane preference: AMP07 (Degli Esposti et al., 1990)
FASG760105 pK-C (Fasman, 1976)
GEIM800109 Aperiodic indices for alpha-proteins (Geisow-Roberts, 1980)
ISOY800108 Normalized relative frequency of coil (Isogai et al., 1980)
JOND750102 pK (-COOH) (Jones, 1975)
KHAG800101 The Kerr-constant increments (Khanarian-Moore, 1980)
MAXF760104 Normalized frequency of left-handed alpha-helix (Maxfield-Scheraga, 1976)
PALJ810113 Normalized frequency of turn in all-alpha class (Palau et al., 1981)
RACS820114 Value of theta(i-1) (Rackovsky-Scheraga, 1982)
RICJ880106 Relative preference value at N3 (Richardson-Richardson, 1988)
ROBB760111 Information measure for C-terminal turn (Robson-Suzuki, 1976)
VHEG790101 Transfer free energy to lipophilic phase (von Heijne-Blomberg, 1979)
WERD780103 Free energy change of alpha(Ri) to alpha(Rh) (Wertz-Scheraga, 1978)
WOLR810101 Hydration potential (Wolfenden et al., 1981)
YUTK870104 Activation Gibbs energy of unfolding, pH9.0 (Yutani et al., 1987)
AURR980103 Normalized positional residue frequency at helix termini N" (Aurora-Rose, 1998)
KUMS000103 Distribution of amino acid residues in the alpha-helices in thermophilic proteins (Kumar et al., 2000)
KUHL950101 Hydrophilicity scale (Kuhn et al., 1995)
ENGD860101 Hydrophobicity index (Engelman et al., 1986)

[Back to content]


The procedures for submitting peptides for prediction

Step 1. Input one sequence of MHC binding peptide into the textbox

    Or upload a file of multiple sequences (One sequence per line)

    This is an example file content of multple sequence (One sequence per line)
   
Step 2. Select the MHC class associated with peptides

Step 3. Press the button of Click to predict peptide immunogenicity

Step 4. Results are shown in the page after a few seconds.

You can also right click on the link "Download CSV file" to save the prediction results on your disk

[Back to content]


Cite POPI

Tung, C.-W. and Ho, S.-Y. (2007) POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. Bioinformatics, 23(8):942-949.

[Back to content]

-->