Dataset Viewer
Ribozyme
stringlengths 2
37
| Organism
stringclasses 56
values | Variable_reactant
stringlengths 2
100
⌀ | Kobs
stringlengths 1
19
⌀ | Unit_Kobs
stringclasses 11
values | km
stringclasses 287
values | Unit_Km
stringclasses 11
values | kcat
stringclasses 262
values | Unit_Kcat
stringclasses 9
values | km_kcat
stringlengths 1
16
⌀ | Unit_Kcat/Km
stringclasses 30
values | Kcleav
stringclasses 52
values | Unit_Kcleav
stringclasses 3
values | Commentary[Temp]
stringclasses 29
values | Commentary[pH]
stringclasses 34
values | Commentary[Mutant]
stringlengths 2
89
⌀ | Commentary[Others]
stringlengths 3
94
⌀ | pubmed_id
stringclasses 164
values | Source
stringclasses 4
values |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Hammerhead | NA | S13 | NA | NA | 38 | nM | 0.4 | min^-1 | 10 | min^-1 µM^-1 | NA | NA | 30°C | 8 | WT | 10 mM MgCl2 | 1280808 | Table |
Hammerhead | NA | S13 | NA | NA | 59 | nM | 8.9 | min^-1 | 150 | min^-1 µM^-1 | NA | NA | 30°C | 8 | DNA-armed | 10 mM MgCl2 | 1280808 | Table |
rz.GH | NA | rGAG | NA | NA | 38 | nM | 0.019 | /min | NA | NA | NA | NA | 55°C | 8.5 | WT | NA | 1408757 | Table |
rz.GH | NA | dGAGrUCA | NA | NA | 56 | nM | 0.087 | /min | NA | NA | NA | NA | 55°C | 8.5 | WT | NA | 1408757 | Table |
rz.DRD | NA | rGAG | NA | NA | 64 | nM | 0.019 | /min | NA | NA | NA | NA | 55°C | 8.5 | DNA in base-pairing sequences and stem-loop II | NA | 1408757 | Table |
rz.DRD | NA | dGAGrUCA | NA | NA | 196 | nM | 0.024 | /min | NA | NA | NA | NA | 55°C | 8.5 | DNA in base-pairing sequences and stem-loop II | NA | 1408757 | Table |
rz.DRD | NA | dGAGrUCA | NA | NA | 48 | nM | 0.012 | /min | NA | NA | NA | NA | 50°C | 8.5 | DNA in base-pairing sequences and stem-loop II | NA | 1408757 | Table |
rz.RLoop | NA | rGAG | NA | NA | 64 | nM | 0.126 | /min | NA | NA | NA | NA | 55°C | 8.5 | DNA in base-pairing sequences only | NA | 1408757 | Table |
rz.RLoop | NA | dGAGrUCA | NA | NA | 91 | nM | 0.108 | /min | NA | NA | NA | NA | 55°C | 8.5 | DNA in base-pairing sequences only | NA | 1408757 | Table |
rz.GH | NA | rGAG | NA | NA | NA | NA | 0.02 | /min | NA | NA | NA | NA | 55°C | 8.5 | WT | NA | 1408757 | Text |
RZ1 | NA | α-lac mRNA | NA | NA | 0.17 | µM | 0.3 | mol/min | 1.8 | µM^-1min^-1 | NA | NA | 37°C | 8 | WT | 20 mM MgCl2 | 1425576 | Table |
RZ2 | NA | α-lac mRNA | NA | NA | 0.27 | µM | 0.4 | mol/min | 1.5 | µM^-1min^-1 | NA | NA | 37°C | 8 | WT | 20 mM MgCl2 | 1425576 | Table |
RZ3 | NA | α-lac mRNA | NA | NA | 0.62 | µM | 1.1 | mol/min | 1.8 | µM^-1min^-1 | NA | NA | 37°C | 8 | WT | 20 mM MgCl2 | 1425576 | Table |
RZ4a | NA | α-lac mRNA | NA | NA | 0.28 | µM | 0.3 | mol/min | 1.1 | µM^-1min^-1 | NA | NA | 37°C | 8 | WT | 20 mM MgCl2 | 1425576 | Table |
RZ4b | NA | α-lac mRNA | NA | NA | 0.28 | µM | 0.5 | mol/min | 1.8 | µM^-1min^-1 | NA | NA | 37°C | 8 | WT | 20 mM MgCl2 | 1425576 | Table |
RZ5 | NA | α-lac mRNA | NA | NA | 0.41 | µM | 1.5 | mol/min | 3.7 | µM^-1min^-1 | NA | NA | 37°C | 8 | WT | 20 mM MgCl2 | 1425576 | Table |
Hammerhead | NA | NA | NA | NA | 0.88 | µM | 0.94 | min^-1 | 1100 × 10^-3 | µM^-1min^-1 | NA | NA | 55°C | 8 | WT | 10 mM Mg^2+ | 1570323 | Table |
Hammerhead | NA | NA | NA | NA | 4.2 | µM | 0.014 | min^-1 | 3.3 × 10^-3 | µM^-1min^-1 | NA | NA | 55°C | 8 | I^10 | 10 mM Mg^2+ | 1570323 | Table |
Hammerhead | NA | NA | NA | NA | 6.9 | µM | 0.0057 | min^-1 | 0.82 × 10^-3 | µM^-1min^-1 | NA | NA | 55°C | 8 | dG^10 | 10 mM Mg^2+ | 1570323 | Table |
Hammerhead | NA | NA | NA | NA | 13 | µM | 0.048 | min^-1 | 3.5 × 10^-3 | µM^-1min^-1 | NA | NA | 55°C | 8 | dG^13 | 10 mM Mg^2+ | 1570323 | Table |
Hammerhead 6 | NA | NA | NA | NA | 46 | nM | 1.5 | min^-1 | 0.032 | nM^-1·min^-1 | NA | NA | 25°C | 7.5 | NA | 10 mM MgCl2 | 1689847 | Table |
Hammerhead 8 | NA | NA | NA | NA | 41 | nM | 1 | min^-1 | 0.024 | nM^-1·min^-1 | NA | NA | 25°C | 7.5 | NA | 10 mM MgCl2 | 1689847 | Table |
Hammerhead 9 | NA | NA | NA | NA | 160 | nM | 1.5 | min^-1 | 0.0093 | nM^-1·min^-1 | NA | NA | 25°C | 7.5 | NA | 10 mM MgCl2 | 1689847 | Table |
Hammerhead 10 | NA | NA | NA | NA | 2300 | nM | 1 | min^-1 | 0.00044 | nM^-1·min^-1 | NA | NA | 25°C | 7.5 | NA | 10 mM MgCl2 | 1689847 | Table |
Hammerhead | NA | NA | NA | NA | 154 | nM | 2.31 | min^-1 | 15 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | WT | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 41 | nM | 0.006 | min^-1 | 0.1 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dG10 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 308 | nM | 0.04 | min^-1 | 0.2 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FG10 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 153 | nM | 0.8 | min^-1 | 1.2 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-NG10 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 51 | nM | 0.005 | min^-1 | 0.1 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dG13 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 227 | nM | 0.008 | min^-1 | 0.04 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FG13 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 190 | nM | 0.16 | min^-1 | 0.8 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-NG13 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 158 | nM | 3.29 | min^-1 | 20.8 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dG19 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 176 | nM | 2.8 | min^-1 | 15.9 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FG19 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 95 | nM | 1.21 | min^-1 | 12.7 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-NG19 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 87 | nM | 1.3 | min^-1 | 14.9 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dG24 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 116 | nM | 2.8 | min^-1 | 24 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FG24 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 66 | nM | 0.83 | min^-1 | 12.6 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-NG24 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 242 | nM | 4.78 | min^-1 | 19.8 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dG27 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 210 | nM | 0.3 | min^-1 | 1.4 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FG27 | 10 mM MgCl2 | 1736306 | Table |
Hammerhead | NA | NA | NA | NA | 136 | nM | 0.92 | min^-1 | 6.8 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-NG27 | 10 mM MgCl2 | 1736306 | Table |
NS83 | Tobacco ringspot virus satellite RNA | YOKS501 | NA | NA | 0.025 | µM | 0.033 | min^-1 | 1.32 | µM^-1min^-1 | NA | NA | 37°C | 7.6 | NA | 12 mM MgCl2, 2 mM spermidine | 1762907 | Table |
NS80 | Tobacco ringspot virus satellite RNA | YOKS403 | NA | NA | 0.023 | µM | 0.008 | min^-1 | 0.33 | µM^-1min^-1 | NA | NA | 37°C | 7.6 | NA | 12 mM MgCl2, 2 mM spermidine | 1762907 | Table |
(-)sTRSV | Tobacco ringspot virus satellite RNA | NA | NA | NA | 0.03 | µM | 2.1 | min^-1 | 70 | µM^-1min^-1 | NA | NA | NA | NA | WT | NA | 1762907 | Table |
Hammerhead | NA | NA | NA | NA | 0.62 | µM | 0.5 | min^-1 | 0.81 | µM^-1min^-1 | NA | NA | 55°C | NA | NA | NA | 1762907 | Multisource |
Hammerhead Ribozyme | NA | NA | NA | NA | 220 | nM | 41 | min^-1 | 186 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E_unmodified | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 217 | nM | 2.8 | min^-1 | 13 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E_unmodified | Mg^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 276 | nM | 0.2 | min^-1 | 1 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_total | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 107 | nM | 0.7 | min^-1 | 7 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_22,28-30 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 187 | nM | 10 | min^-1 | 53 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_11,14 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 269 | nM | 38 | min^-1 | 140 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_14 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 321 | nM | 4 | min^-1 | 12 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_14 | Mg^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 243 | nM | 22 | min^-1 | 90 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_28 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 187 | nM | 16 | min^-1 | 86 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_29 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 91 | nM | 4 | min^-1 | 44 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-FA_30 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 157 | nM | 0.6 | min^-1 | 4 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dA_total | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 133 | nM | 8 | min^-1 | 57 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dA_11,14 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 264 | nM | 21 | min^-1 | 79 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dA_14 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 168 | nM | 14 | min^-1 | 86 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dA_28 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 179 | nM | 20 | min^-1 | 114 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dA_29 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 58 | nM | 5 | min^-1 | 89 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E-dA_30 | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 178 | nM | 22 | min^-1 | 120 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E2_unmodified | Mn^2+ | 1911762 | Table |
Hammerhead Ribozyme | NA | NA | NA | NA | 184 | nM | 25 | min^-1 | 136 | µM^-1·min^-1 | NA | NA | 25°C | 7.5 | E2-FA_20-22 | Mn^2+ | 1911762 | Table |
Hammerhead | Lucerne transient streak virus | S | NA | NA | 1.3 | µM | 0.5 | min^-1 | NA | NA | NA | NA | 50°C | 8.5 | WT | 20 mM MgCl2, S concentration 0.05-0.6 µM | 2646593 | Table |
Hammerhead | minus avocado sunbloth viroid | S | NA | NA | 0.63 | µM | 0.5 | min^-1 | NA | NA | NA | NA | 50°C | 8.5 | WT | 20 mM MgCl2 | 2646593 | Table |
Hammerhead | Lucerne transient streak virus | S | NA | NA | 7.5 | µM | NA | NA | NA | NA | NA | NA | 50°C | 8.5 | WT | 20 mM MgCl2, S concentration >0.6 µM | 2646593 | Text |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.63 | min^-1 | 25 | µM | 0.8 | min^-1 | 32x10^3 | M^-1·min^-1 | NA | NA | 30°C | 7.5 | WT | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Multisource |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.14 | min^-1 | 41 | µM | 0.27 | min^-1 | 6.6x10^3 | M^-1·min^-1 | NA | NA | 30°C | 7.5 | C109G | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Multisource |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.0027 | min^-1 | 120 | µM | 0.0072 | min^-1 | 0.06x10^3 | M^-1·min^-1 | NA | NA | 30°C | 7.5 | G212C | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Multisource |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.0071 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 30°C | 7.5 | C109G:G212C | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Table |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.047 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 30°C | 7.5 | G212A | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Table |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.12 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 30°C | 7.5 | C211G | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Table |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.047 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 30°C | 7.5 | ∆A210 | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Table |
Tetrahymena IVS | Tetrahymena thermophila | 32P-labeled RNA | 0.002 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 30°C | 7.5 | C109G:C211G | 200 mM NaCl, 6 mM MgCl2 | 2684642 | Table |
Tetrahymena ribozyme | Tetrahymena thermophila | 32P-labeled RNA | 0.48 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 42°C | 7.5 | G212C | 200 mM NaCl, 10 mM MgCl2 | 2684642 | Text |
Hammerhead | NA | NA | NA | NA | 0.8 | µM | 0.29 | min^-1 | 0.36 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | WT | 10 mM Mg^2+ | 7487885 | Table |
Hammerhead | NA | NA | NA | NA | 0.5 | µM | 0.04 | min^-1 | 0.08 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | ^4H^C_3 | 10 mM Mg^2+ | 7487885 | Table |
Hammerhead | NA | NA | NA | NA | 2.5 | µM | 0.046 | min^-1 | 0.019 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | ^4H^C_4 | 10 mM Mg^2+ | 7487885 | Table |
Hammerhead | NA | NA | NA | NA | 0.7 | µM | 0.096 | min^-1 | 0.14 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | ^4S^U_4 | 10 mM Mg^2+ | 7487885 | Table |
Hammerhead | NA | NA | NA | NA | 0.7 | µM | 0.2 | min^-1 | 0.27 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | ^4H^C_7 | 10 mM Mg^2+ | 7487885 | Table |
Hammerhead | NA | NA | NA | NA | 1 | µM | 0.19 | min^-1 | 0.19 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | ^4S^U_16.1 | 10 mM Mg^2+ | 7487885 | Table |
Hammerhead | NA | NA | NA | NA | 2.3 | µM | 0.083 | min^-1 | 0.037 | min^-1 µM^-1 | NA | NA | 37°C | 7.9 | ^4H^C_17 | 10 mM Mg^2+ | 7487885 | Table |
Hairpin | Tobacco ringspot virus | sTRSV-C8A | NA | NA | 2500 | nM | 0.038 | min^-1 | 2 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUA | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Tobacco ringspot virus | sTRSV | NA | NA | 96 | nM | 0.36 | min^-1 | 360 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUC | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Tobacco ringspot virus | sTRSV-C8G | NA | NA | 540 | nM | 0.01 | min^-1 | 2 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUG | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Tobacco ringspot virus | sTRSV-C8U | NA | NA | 390 | nM | 0.045 | min^-1 | 12 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUU | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Chicory yellow mottle virus | sCYMV1 | NA | NA | 400 | nM | 0.32 | min^-1 | 80 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUA | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Chicory yellow mottle virus | sCYMV1-A8C | NA | NA | 1500 | nM | 0.14 | min^-1 | 9 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUC | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Chicory yellow mottle virus | sCYMV1-A8G | NA | NA | >6500 | nM | NA | NA | NA | NA | NA | NA | 37°C | 7.5 | GUG | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Chicory yellow mottle virus | sCYMV1-A8U | NA | NA | >10000 | nM | NA | NA | NA | NA | NA | NA | 37°C | 7.5 | GUU | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Chicory yellow mottle virus | sArMV | NA | NA | 1400 | nM | 0.19 | min^-1 | 14 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUA | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Arabis mosaic virus | sArMV-A1C | NA | NA | 880 | nM | 0.26 | min^-1 | 30 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUA | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Arabis mosaic virus | sArMV-A1C-A8C | NA | NA | 5400 | nM | 0.22 | min^-1 | 4 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUC | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Arabis mosaic virus | sArMV-A1C-A8G | NA | NA | 1700 | nM | 0.26 | min^-1 | 15 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUG | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Arabis mosaic virus | sArMV-A1C-A8U | NA | NA | 3000 | nM | 0.4 | min^-1 | 13 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUU | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
Hairpin | Arabis mosaic virus | sArMV | NA | NA | 2600 | nM | 0.29 | min^-1 | 11 | 10^4 M^-1 min^-1 | NA | NA | 37°C | 7.5 | GUA | 12 mM MgCl2, 2 mM spermidine | 7495810 | Table |
R32 | NA | all-RNA substrat | 0.26 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 37°C | 7 | WT | 25 mM CoCl2 | 7506830 | Table |
DRD32 | NA | all-RNA substrat | 0.53 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 37°C | 7 | Chimeric DNA/RNA | 25 mM CoCl2 | 7506830 | Table |
R32 | NA | all-RNA substrat | 0.58 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 37°C | 7 | WT | 25 mM MgCl2 | 7506830 | Table |
DRD32 | NA | all-RNA substrat | 1.5 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 37°C | 7 | Chimeric DNA/RNA | 25 mM MgCl2 | 7506830 | Table |
R32 | NA | all-RNA substrat | 0.61 | min^-1 | NA | NA | NA | NA | NA | NA | NA | NA | 37°C | 7 | WT | 25 mM MgSO4 | 7506830 | Table |
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🚩Citation
Please cite the following paper if you use jackkuo/LLM-Ribozyme-Kinetics-Golden-Benchmark in your work.
@article {Jiang2025.03.03.641178,
author = {Jiang, Jinling and Hu, Jie and Xie, Siwei and Guo, Menghao and Dong, Yuhang and Fu, Shuai and Jiang, Xianyue and Yue, Zhenlei and Shi, Junchao and Zhang, Xiaoyu and Song, Minghui and Chen, Guangyong and Lu, Hua and Wu, Xindong and Guo, Pei and Han, Da and Sun, Zeyi and Qiu, Jiezhong},
title = {Enzyme Co-Scientist: Harnessing Large Language Models for Enzyme Kinetic Data Extraction from Literature},
elocation-id = {2025.03.03.641178},
year = {2025},
doi = {10.1101/2025.03.03.641178},
publisher = {Cold Spring Harbor Laboratory},
abstract = {The extraction of molecular annotations from scientific literature is critical for advancing data-driven research. However, traditional methods, which primarily rely on human curation, are labor-intensive and error-prone. Here, we present an LLM-based agentic workflow that enables automatic and efficient data extraction from literature with high accuracy. As a demonstration, our workflow successfully delivers a dataset containing over 91,000 enzyme kinetics entries from around 3,500 papers. It achieves an average F1 score above 0.9 on expert-annotated subsets of protein enzymes and can be extended to the ribozyme domain in fewer than 3 days at less than $90. This method opens up new avenues for accelerating the pace of scientific research.Competing Interest StatementThe authors have declared no competing interest.},
URL = {https://www.biorxiv.org/content/early/2025/03/11/2025.03.03.641178},
eprint = {https://www.biorxiv.org/content/early/2025/03/11/2025.03.03.641178.full.pdf},
journal = {bioRxiv}
}
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