System and method for identifying t cell and other epitopes and the like
OwnerRoland Martin, Richard Simon +3inventors
InventorsRoland Martin, Richard Simon, Yingdong Zhao, Bruno Gran, Clemencia Pinilla
Life of this patent
Estimating the term…
Abstract
A system and method is described for identifying T cell and other epitopes and the like.
Claims41
A method of determining the amino acid sequence of a peptide that stimulates a functional response, comprising:
- identifying at least a first and a second amino acid position of the peptide;
- defining a stimulating potency level of each of a plurality of amino acids within the first position of the peptide;
- defining a stimulatory potency level of each of a plurality of amino acids within the second position of the peptide;
- and
- evaluating selected positions of a protein with the at least first and second positions of the peptide to determine the stimulatory potency level of amino acids in said selected positions.
A method of determining the amino acid sequence of a peptide that stimulates a functional response, comprising
- identifying a position of the peptide;
- testing each amino acid on the identified position so as to define a stimulatory potency level for each of said amino acids;
- and
- selecting one of the amino acids, based upon its defined stimulatory potency level, as the amino acid in said position which produces the greatest stimulatory potency.
A method of determining the amino acid sequence of a peptide that stimulates a functional response comprising:
- identifying a selected number of positions of the peptide;
- and
- testing each amino acid on each identified position so as to define a stimulatory potency level for each of said amino acids.
A method of scoring the ability of amino acids within a position on a peptide to stimulate a functional response, comprising:
- conducting a plurality of measurements of the stimulation value of each of said amino acids within a position on the peptide;
- identifying a mean value (L) for said measurements;
- identifying a value for background noise in said measurements (B);
- and
- identifying a smoothed estimate of a standard deviation std(L) and std(13) for each of said measurements;
- determining a score for each of the i amino acids within said position using the relationship:
- 11 S i = L i - B ( std ( L i ) ) 2 + ( std ( B ) ) 2
A method of evaluating a protein to identify a peptide having a desired level of stimulatory potency, comprising:
- providing a peptide having a defined number of positions;
- scoring the stimulatory potency of each plurality of amino acids in each plurality of the positions with respect to a functional response;
- defining a template including the scores of the amino acids in each of the positions;
- applying the scores of the template to amino acids in corresponding positions on selected portions of the protein;
- summing amino acid scores at each of a plurality of portions of the protein, to produce a stimulatory potency score for each of said portions;
- and
- comparing the stimulatory potency scores for each of said portions so as to identify a portion of the protein having a desired level of stimulatory potency.
A method for determining the amino acid sequence of a peptide that stimulates a T cell, comprising:
- providing a panel of peptides;
- scoring the ability of each amino acid within said panel of peptides to stimulate a T cell;
- and
- determining the amino acid sequence of the peptide that most effectively stimulates said T cell.
A method for determining a protein that stimulates a T cell, comprising:
- providing a plurality of peptides, wherein each peptide comprises a different amino acid sequence;
- measuring the stimulatory potential of each peptide in said plurality of peptides for its ability to stimulate said T cell;
- determining a first peptide in said plurality of peptides that most effectively stimulates said T cell;
- and
- searching a database of protein sequences to identify a protein having the amino acid sequence of said first peptide.
Dependencies are inferred from the claim text.