HUT2 = HIP2 + HAPTIC3 + HEPTAD2 + SETH

HAPTIC3: Heuristic Affinity Prediction Tool for Immune Complexes 3

Use HAPTIC3 to estimate affinity of paratopes for cognate disordered peptidic antigens in a solvent system characterized by temperature, pH, ionic strength, relative permittivity (i.e., dielectric constant), dipole-ion cutoff distance and donor/acceptor parameters for hydrogen-bonding/similar interactions, allowing for variable-length B-cell epitopes with conformational flexibility unconstrained by covalent modifications such as disulfide bonds (cf. HEPTAD2).

Parameter/Process: Immunization: Immunoassay:
Paratope-footprint radius (Å): (same as for immunization)
Temperature (K):
pH (= -log10[H+]):
Ionic strength (M):
Relative permittivity:
Dipole-ion cutoff distance (Å):
Donor (alpha) parameter:
Acceptor (beta) parameter:
Input peptidic sequence data (FASTA format):

Notes:

  1. HAPTIC3 estimates epitope-paratope binding affinity as dissocation-constant values for variable-length candidate epitopes of disordered peptidic antigen sequences that are devoid of disulfide bonds (cf. HEPTAD2), in a solvent system characterized by temperature, pH, ionic strength, relative permittivity (i.e., dielectric constant), dipole-ion cutoff distance and donor/acceptor parameters for hydrogen-bonding/similar interactions.
  2. Paratope-footprint radius (in Å) determines maximum length of rigid poly-L-proline II (PPII) helical segment (assuming 3.1 Å rise per residue) in a candidate epitope.
  3. Temperature of immunization is normal body temperature for immunized animal species (e.g., 310.15 K = 37°C for human/mouse [default] or 312.35 K = 39.2°C for rabbit).
  4. Temperature of immunoassay is for experiment to measure epitope-paratope binding affinity, with default value assumed for ambient/room temperature of 298.15K = 25°C.
  5. Default pH = 7.4 is for normal adult human blood plasma.
  6. Other default solvent-system parameter values are for 0.15 M aqueous NaCl (i.e., plain normal saline) solution as estimated using SETH (with only relative permittivity assumed to be temperature-dependent).
  7. Input must be provided as peptidic sequence data in FASTA format using only the 20 standard amino-acid residue codes (ACDEFGHIKLMNPQRSTVWY), such that only upper-case letter codes are considered in generating candidate epitopes while lower-case letter codes (e.g., introduced by HIP2 to represent excluded residues) are neglected.
  8. Each input sequence is partitioned into candidate epitopes (i.e., tripeptide and longer segments).
  9. Excessively long candidate epitopes (i.e., comprising excessively long run/s of consecutive proline residues and/or deemed too bulky to fit paratope) are excluded from analysis.
  10. Candidate epitopes are ranked by estimated affinity at temperature of immunization, such that top-ranking candidate epitope is identified as predicted most immunodominant epitope.