Table 3.
Sequence Design Identity Recovery and PSSM Recovery for All Amino Acidsa
| score function | ARG | LYS | HIS | PHE | TRP | TYR | CYS | MET | ALA | ILE | LEU | VAL | GLY | PRO | SER | THR | ASN | GLN | ASP | GLU | Total Averaqe | PSSM Recovery | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| score 12’ | 43% | 37% | 49% | 64% | 58% | 44% | 45% | 38% | 64% | 67% | 68% | 63% | 79% | 82% | 47% | 50% | 28% | 21% | 52% | 37% | 57% | 75% | |
| Core | Talaris2014 | 39% | 40% | 43% | 65% | 52% | 48% | 60% | 51% | 63% | 73% | 82% | 78% | 92% | 88% | 59% | 65% | 54% | 37% | 57% | 36% | 64% | 79% |
| PCI | 42% | 42% | 42% | 64% | 64% | 54% | 45% | 38% | 68% | 69% | 67% | 65% | 83% | 87% | 50% | 59% | 50% | 36% | 60% | 44% | 61% | 75% | |
| score 12’ | 25% | 24% | 16% | 32% | 38% | 37% | 30% | 10% | 16% | 33% | 36% | 34% | 81% | 73% | 36% | 40% | 27% | 20% | 35% | 24% | 36% | 70% | |
| Surface | Talaris2014 | 35% | 32% | 20% | 31% | 42% | 42% | 31% | 12% | 13% | 35% | 44% | 36% | 81% | 80% | 36% | 34% | 36% | 21% | 46% | 33% | 40% | 73% |
| PCI | 31% | 36% | 22% | 33% | 30% | 41% | 38% | 13% | 22% | 37% | 45% | 34% | 84% | 81% | 41% | 43% | 34% | 19% | 43% | 26% | 41% | 69% | |
| score 12’ | 33% | 29% | 35% | 58% | 54% | 43% | 43% | 30% | 48% | 61% | 62% | 57% | 80% | 77% | 41% | 45% | 27% | 20% | 41% | 28% | 48% | 72% | |
| Overall | Talaris2014 | 40% | 33% | 34% | 66% | 63% | 49% | 43% | 35% | 53% | 68% | 74% | 65% | 82% | 84% | 39% | 45% | 40% | 27% | 48% | 37% | 54% | 77% |
| PCI | 36% | 38% | 34% | 58% | 57% | 51% | 44% | 30% | 52% | 64% | 63% | 59% | 84% | 83% | 45% | 52% | 40% | 27% | 49% | 32% | 53% | 72% |
a
Sequence design for all amino acids using score12’, Talaris2014, or PCI. Proteins were completely redesigned, and the recovery of the native amino acid at a given position was measured. For PSSM recovery, a position was labeled as “recovered” if the residue selected by design was sampled by evolution at the same position. Recovery is broken out by core and surface residues, in addition to showing overall recovery. Surface residues are defined as residues with 16 or less neighbors; core residues have more than 16 neighbors.