Spacio-temporal determination of polypeptide structure
AssigneePeptone, LTD.
InventorsOliver DUTTON, Carlo FISICARO, Matthew Michael HEBERLING, Louie Derek HENDERSON, Istvan REDL, Kamil TAMIOLA
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Abstract
Disclosed herein are methods of in silico generation of polypeptide structures using time-based data generated from molecular dynamics simulations. Also disclosed herein are methods of predicting an epitope or binding surface of a polypeptide using in silico methods. Also disclosed herein are compositions containing polypeptide therapeutics designed to bind to a predicted epitope structure of a polypeptide, as well as methods of treating a subject by administering to the subject compositions containing the same.
Claims24
-16. (canceled)
A method of generating an epitope structure, the method comprising:
- a) providing a polypeptide sequence;
- b) calculating index scores for a plurality of epitope structures in the polypeptide sequence, wherein the index scores are calculated based on at least two of:
- a structural prominence parameter, a disorder parameter, or a conservation parameter of the epitope, wherein:
- (i) the conservation parameter is calculated based on conservation of at least two amino acid residues in a multiple sequence alignment comprising the target polypeptide;
- (ii) the disorder parameter and the structural prominence parameter are derived from a molecular dynamics (MD) simulation of a homology model comprising aggregate structures of homologs of the target polypeptide;
- and
- (iii) the index scores are proportional to the structural prominence parameter and the conservation parameter, and are inversely proportional to the disorder parameter;
- and
- c) ranking the index scores to select an epitope structure among the plurality of epitope structures having the highest index score.
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Dependencies are inferred from the claim text.