Table 3.
A comparison of protein tertiary structure prediction accuracies with different homology modeling servers available in public domain
| Sl. No. | PDB ID | CPHModels (19) RMSD (Å) | SwissModel (4) RMSD (Å) | EsyPred3D (38) RMSD (Å) | ModWeb (21) RMSD (Å) | Geno3D (39) RMSD (Å) | 3DJigSaw (40) RMSD (Å) | Bhageerath RMSD (Å) |
|---|---|---|---|---|---|---|---|---|
| 1 | 1E0Q(1–17) | — | — | 1.7 (1–17) | — | — | 1.5 (1–16) | 2.5 |
| 2 | 1B03(1–18) | — | — | 3.5 (2–18) | — | — | — | 4.4 |
| 3 | 1WQC(1–26) | 0.5 (1–26) | 0.4 (1–26) | — | — | — | — | 2.5 |
| 4 | 1RJU(1–36) | 2.0 (1–36) | 1.7 (1–36) | 2.1 (1–36) | — | — | — | 5.9 |
| 5 | 1EDM(1–39) | 1.5 (1–39) | 1.4 (1–39) | 0.8 (2–38) | 0.5 (1–39) | — | 1.8 (1–39) | 3.5 |
| 6 | 1AB1(1–46) | 0.6 (1–46) | 2.8 (1–46) | 0.4 (1–46) | 0.4 (1–46) | 0.7 (1–46) 0.7 (1–46) | — | 2.9 |
| 7 | 1BX7(1–51) | 0.6 (1–51) | 0.8 (1–51) | 2.2 (3–50) | 0.6 (1–51) | 2.6 (4–51) | 2.2 (3–50) | 3.1 |
| 8 | 1B6Q(1–56) | 4.7 (1–56) | 5.0 (1–56) | 2.7 (3–56) | 5.1 (1–56) | 0.7 (1–56) 1.4 (1–56) | 4.8 (1–56) | 3.1 |
| 9 | 1ROP(1–56) | 1.3 (1–56) | 0.6 (1–56) | 4.7 (3–56) | 0.7 (1–56) | 0.7 (1–56) 0.8 (1–56) | 1.3 (1–56) | 4.3 |
| 10 | 1NKD(1–59) | 0.5 (1–59) | 7.7 (1–50) | 0.6 (1–59) | 1.9 (1–59) 0.7 (1–59) | 1.3 (1–59) 1.2 (1–59) | 0.4 (1–59) | 3.8 |
| 11 | 1RPO(1–61) | 0.5 (1–61) | 7.7 (1–50) | 0.5 (1–59) | 1.9 (1–61) 0.7 (1–59) | 0.8 (1–61) 0.9 (1–61) | 0.4 (1–61) | 3.8 |
| 12 | 1QR8(1–68) | 0.5 (1–68) | 0.5 (1–68) | 1.1 (2–66) | 1.6 (1–68) | 0.9 (1–68) 1.2 (1–68) | 0.5 (1–68) | 4.4 |
| 13 | 1FME(1–28) | 0.7 (1–28) | 0.9 (1–28) | — | — | — | — | 3.7 |
| 14 | 1ACW(1–29) | 0.7 (1–29) | 0.4 (1–29) | — | — | — | — | 5.1 |
| 15 | 1DFN(1–30) | 0.8 (1–30) | 0.4 (1–30) | 1.3 (2–30) | — | — | — | 5.0 |
| 16 | 1Q2K(1–31) | 0.9 (1–31) | 0.5 (1–31) | — | — | — | — | 4.2 |
| 17 | 1SCY(1–31) | 0.6 (1–31) | 0.7 (1–31) | — | — | — | — | 3.1 |
| 18 | 1XRX(1–34) | 0.5 (1–34) | 0.3 (1–34) | — | 0.7 (1–34) | — | 3.1 (1–31) | 5.6 |
| 19 | 1ROO(1–35) | 0.8 (1–35) | 0.7 (1–35) | — | — | — | — | 2.8 |
| 20 | 1YRF(1–35) | 1.6 (1–35) | 0.5 (1–35) | 1.2 (1–35) | 1.3 (1–35) | — | — | 4.8 |
| 21 | 1YRI(1–35) | 1.7 (1–35) | 0.7 (1–35) | 1.4 (1–35) | 1.5 (1–35) | — | — | 3.8 |
| 22 | 1VII(1–36) | 2.4 (2–36) | 0.9 (1–36) | 2.2 (2–36) | 2.0 (2–36) | — | — | 3.7 |
| 23 | 1BGK(1–37) | 0.8 (1–37) | 0.5 (1–37) | – | 0.7 (1–37) | — | — | 4.1 |
| 24 | 1BHI(1–38) | 0.8 (1–38) | 0.4 (1–38) | 1.0 (1–38) | 1.1 (1–38) | — | — | 5.3 |
| 25 | 1OVX(1–38) | 0.9 (1–38) | 0.3 (1–38) | 1.0 (1–38) | 0.6 (1–38) | — | 0.3 (1–38) | 4.0 |
| 26 | 1I6C(1–39) | 4.2 (1–39) | 4.4 (1–39) | 4.5 (1–39) | 0.8 (1–39) | — | 3.1 (1–34) | 5.1 |
| 27 | 2ERL(1–40) | 1.3 (1–40) | 0.9 (1–40) | 0.4 (1–40) | 0.4 (1–40) | 1.2 (1–40) 1.1 (1–40) | — | 3.2 |
| 28 | 1RES(1–43) | 4.2 (1–43) | 4.1 (1–43) | 4.2 (1–43) | 0.8 (1–43) | 1.2 (1–43) 1.1 (1–43) | — | 4.2 |
| 29 | 2CPG(1–43) | 0.8 (1–43) | 0.6 (1–43) | 1.1 (1–43) | 0.9 (1–43) | 0.9 (1–43) | 0.6 (1–43) | 5.3 |
| 30 | 1DV0(1–45) | 4.2 (1–45) | 10.5 (1–35) | 2.0 (1–42) | 0.7 (1–45) 2.4 (1–44) | 0.9 (1–45) 1.1 (1–45) | 0.6 (1–45) | 5.1 |
| 31 | 1IRQ(1–48) | 0.6 (1–48) | 0.8 (1–48) | 1.3 (2–48) | 0.7 (1–48) | 1.2 (1–48) | 0.9 (1–48) | 5.3 |
| 32 | 1GUU(1–50) | 2.5 (1–50) | 2.6 (1–50) | 2.3 (38–50) | 5.7 (1–50) 0.5 (1–50) 2.2 (1–49) | 1.5 (1–48) 1.6 (1–48) | 1.6 (1–42) | 4.6 |
| 33 | 1GV5(1–52) | 1.4 (1–52) | 0.6 (1–52) | 1.3 (1–52) | 0.68 (1–52) 2.2 (3–52) | 2.1 (3–46) 2.0 (3–46) | 1.8 (3–45) | 4.1 |
| 34 | 1GVD(1–52) | 1.4 (1–52) | 4.2 (1–51) | 1.3 (1–52) | 5.5 (1–52) | 6.6 (1–44) 9.8 (1–44) | 6.4 (1–43) | 4.9 |
| 35 | 1MBH(1–52) | 1.8 (1–52) | 3.3 (1–51) | 1.8 (1–52) | 1.9 (1–52) | 1.6 (1–52) 2.1 (1–52) | 1.1 (6–45) | 4.0 |
| 36 | 1GAB(1–53) | 0.6 (1–53) | 1.6 (1–53) | 3.3 (1–53) | 3.3 (1–53) | 2.2 (1–53) 2.7 (1–53) | 0.5 (1–53) | 3.6 |
| 37 | 1MOF(1–53) | 0.6 (1–53) | 1.8 (1–53) | 1.9 (1–53) | 1.7 (1–53) 2.3 (3–51) | 3.4 (1–53) 3.4 (1–53) | 1.7 (1–53) | 2.9 |
| 38 | 1ENH(1–54) | 0.5 (1–54) | 0.8 (1–54) | 0.9 (3–53) | 1.7 (1–53) 1.0 (5–53) 2.5 (1–54) 3.0 (1–51) | 1.7 (1–54) 1.7 (1–54) | 0.5 (1–54) | 4.6 |
| 39 | 1IDY(1–54) | 4.0 (2–54) | 10.8 (1–50) | 3.8 (2–52) | 0.9 (1–54) | 10.0 (5–46) 10.0 (5–46) | 0.3 (1–54) | 3.5 |
| 40 | 1PRV(1–56) | 5.7 (2–56) | 2.1 (1–56) | 5.6 (3–56) | 1.6 (1–56) | 5.7 (2–56) 5.4 (2–56) | 5.6 (2–56) | 4.9 |
| 41 | 1HDD(1–57) | 13.2 (1–57) | 13.3 (1–57) | 1.2 (1–56) | 2.7 (1–57) 3.3 (1–51) 3.6 (1–57) 1.5 (9–55) 1.3 (1–56) | 2.1 (1–56) 2.7 (1–56) | 0.3 (1–57) | 4.8 |
| 42 | 1BDC(1–60) | 3.4 (1–60) | 2.7 (6–39) 3.1 (1–38) | 2.7 (6–39) | 2.7(5–59) | 2.1 (1–60) 1.8 (1–60) | 2.6 (5–37) | 4.8 |
| 43 | 1I5X(1–61) | 0.7 (1–61) | 1.1 (1–61) | 1.6 (1–61) | 1.8 (1–61) | 1.5 (1–61) 1.4 (1–61) | 0.9 (1–61) | 2.6 |
| 44 | 1I5Y(1–61) | 0.7 (1–61) | 1.1 (1–61) | 1.6 (1–61) | 1.4 (1–61) | 1.7 (1–61) 1.1 (1–61) | 0.9 (1–61) | 2.6 |
| 45 | 1KU3(1–61) | 1.3 (1–61) | 2.8 (4–61) | 1.5 (1–61) | 1.5 (1–61) | 1.9 (1–61) 1.7 (1–61) | 0.4 (1–61) | 5.5 |
| 46 | 1YIB(1–61) | 1.8 (2–61) | 1.7 (1–61) | 3.4 (1–61) | 2.8 (2–60) | 1.5 (1–61) 1.6 (1–61) | 1.9 (2–61) | 3.5 |
| 47 | 1AHO(1–64) | 0.6 (1–64) | 0.5 (1–64) | 1.3 (1–64) | 0.4 (1–64) | 1.8 (1–64) | 0.3 (1–64) | 6.0 |
| 48 | 1DF5(1–68) | 0.6 (1–68) | 1.5 (1–68) | 1.8 (2–66) | 2.2 (1–68) | 1.8 (1–68) 1.8 (1–68) | 1.6 (1–68) | 3.1 |
| 49 | 1QR9(1–68) | 0.5 (1–68) | 0.7 (1–68) | 1.4 (2–66) | 1.8 (1–68) | 1.7 (1–68) 1.8 (1–68) | 0.6 (1–68) | 3.8 |
| 50 | 1AIL(1–70) | 0.87 (1–70) | 0.73 (1–70) | 0.46 (1–70) | 0.6 (1–70) | 0.88 (1–70) 0.97 (1–70) | 0.9 (1–70) | 4.2 |
The numbers in parenthesis indicate the length of the protein model obtained. Supplementary Tables S2–S7 in the supplementary information contain the template ID, % sequence identity and alignment for each method and structure shown above.