Patent ID: 8484010

Claim:
A method for determining an aptamer sequence comprising the steps of: providing a structure of a protein to a computer; individually modeling, with the computer, the entropic probability distribution of four individual potential first nucleotides to the protein and identifying a binding site for each of the four nucleotides; comparing the individual entropic probability distribution of each of the nucleotide-binding site pairings, with the computer, and selecting the pairing that has the most favorable entropic probability distribution for binding, thereby identifying a first nucleotide and its corresponding first binding site; individually modeling the entropic probability distribution of a plurality of different first oligonucleotides to the first binding site, with the computer, the first oligonucleotides each consisting of the first nucleotide plus one potential second nucleotide and thereafter selecting the first oligonucleotide that has the most favorable entropic probability distribution for binding, thereby identifying a second nucleotide; and individually modeling the entropic probability distribution of a plurality of different second oligonucleotides to the first binding site, with the computer, the second oligonucleotides consisting of the first nucleotide plus the second nucleotide disposed adjacent the first, plus one potential third nucleotide and thereafter selecting the second oligonucleotide that has the most favorable entropic probability distribution for binding, thereby identifying a third nucleotide.