Method for determining surface protruding amino acids of a human leukocyte antigen (hla) protein
AssigneePirche AG
InventorMatthias Niemann
Life of this patent
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Abstract
A method for determining an amino acid residue protruding from the surface of a human leukocyte antigen (HLA) protein structure, including: (i) employing an ellipsoid-fitting algorithm to a subset of atoms of an HLA protein structure that are in spatial proximity to each other, (ii) repeating step (i) for multiple subsets of atoms of the HLA protein structure, thereby creating multiple fitted ellipsoids, and (iii) determining whether an amino acid of an HLA protein structure is surface protruding by considering the spatial distribution of atoms of any given amino acid residue relative to the position of the multiple fitted ellipsoids.
Claims20
A method for determining an amino acid residue protruding from the surface of a human leukocyte antigen (HLA) protein structure, comprising:
- (i) employing an ellipsoid-fitting algorithm to a subset of atoms of an HLA protein structure that are in spatial proximity to each other,
- (ii) repeating step (i) for multiple subsets of atoms of the HLA protein structure, thereby creating multiple fitted ellipsoids, and
- (iii) determining whether an amino acid of an HLA protein structure is surface protruding by considering the spatial distribution of atoms of any given amino acid residue relative to the position of the multiple fitted ellipsoids.
A method for predicting a human leukocyte antigen (HLA) B-cell epitope that is mismatched between two or more subjects, comprising:
- i. obtaining biological samples from the two or more subjects,
- ii. determining the amino acid sequences of an HLA protein from the two or more subjects,
- iii. determining one or more mismatched amino acids of the HLA protein between two or more subjects,
- iv. determining whether said mismatched amino acids are predicted to be protruding from a surface of an HLA structure,
- comprising comparing said mismatched amino acids to a database of surface-protruding residues for HLA proteins, wherein the surface-protruding residues of the database are predicted by a neural network trained on amino acids sequences of experimentally determined and predicted HLA protein structures, and on the corresponding residues' surface protrusion,
- v. wherein a mismatched amino acid predicted to be surface protruding indicates a human leukocyte antigen (HLA) B-cell epitope that is mismatched between two or more subjects.
Dependencies are inferred from the claim text.