Dataset Preview
The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 12 new columns ({'km(mM)', 'Commentary[Mutant]', 'Commentary[Cosubstrate]', 'Enzyme', 'km_kcat(mM^-1s^-1)', 'kcat(s^-1)', 'Substrate', 'Organism', 'Reference[Table/Text]', 'ID_gold', 'Commentary[pH]', 'Commentary[Temp]'}) and 18 missing columns ({' Commentary[Mutant] ', ' Unit_Kcat ', 'km_kcat', 'Kcleav', 'kcat', ' Variable_reactant ', ' Commentary[Temp] ', 'Source', ' Unit_Kcleav ', 'Kobs', ' Commentary[Others] ', ' Unit_Km ', ' Ribozyme ', ' Unit_Kcat/Km ', 'km', ' Unit_Kobs ', ' Commentary[pH] ', ' Organism '}).
This happened while the csv dataset builder was generating data using
hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark/Golden Benchmark for Enzyme Kinetics_converted.csv (at revision 47192f5bab5578aeb305f148600563298a34535e)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1870, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, in write_table
pa_table = table_cast(pa_table, self._schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
ID_gold: int64
pubmed_id: int64
Enzyme: string
Organism: string
Substrate: string
km(mM): string
kcat(s^-1): string
km_kcat(mM^-1s^-1): string
Commentary[Temp]: string
Commentary[pH]: string
Commentary[Mutant]: string
Commentary[Cosubstrate]: string
Reference[Table/Text]: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 1886
to
{' Ribozyme ': Value(dtype='string', id=None), ' Organism ': Value(dtype='string', id=None), ' Variable_reactant ': Value(dtype='string', id=None), 'Kobs': Value(dtype='string', id=None), ' Unit_Kobs ': Value(dtype='string', id=None), 'km': Value(dtype='string', id=None), ' Unit_Km ': Value(dtype='string', id=None), 'kcat': Value(dtype='string', id=None), ' Unit_Kcat ': Value(dtype='string', id=None), 'km_kcat': Value(dtype='string', id=None), ' Unit_Kcat/Km ': Value(dtype='string', id=None), 'Kcleav': Value(dtype='string', id=None), ' Unit_Kcleav ': Value(dtype='string', id=None), ' Commentary[Temp] ': Value(dtype='string', id=None), ' Commentary[pH] ': Value(dtype='string', id=None), ' Commentary[Mutant] ': Value(dtype='string', id=None), ' Commentary[Others] ': Value(dtype='string', id=None), 'pubmed_id': Value(dtype='string', id=None), 'Source': Value(dtype='string', id=None)}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1438, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1050, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 924, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1000, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1872, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 12 new columns ({'km(mM)', 'Commentary[Mutant]', 'Commentary[Cosubstrate]', 'Enzyme', 'km_kcat(mM^-1s^-1)', 'kcat(s^-1)', 'Substrate', 'Organism', 'Reference[Table/Text]', 'ID_gold', 'Commentary[pH]', 'Commentary[Temp]'}) and 18 missing columns ({' Commentary[Mutant] ', ' Unit_Kcat ', 'km_kcat', 'Kcleav', 'kcat', ' Variable_reactant ', ' Commentary[Temp] ', 'Source', ' Unit_Kcleav ', 'Kobs', ' Commentary[Others] ', ' Unit_Km ', ' Ribozyme ', ' Unit_Kcat/Km ', 'km', ' Unit_Kobs ', ' Commentary[pH] ', ' Organism '}).
This happened while the csv dataset builder was generating data using
hf://datasets/jackkuo/LLM-Enzyme-Kinetics-Golden-Benchmark/Golden Benchmark for Enzyme Kinetics_converted.csv (at revision 47192f5bab5578aeb305f148600563298a34535e)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Ribozyme
string | Organism
string | Variable_reactant
string | Kobs
string | Unit_Kobs
string | km
string | Unit_Km
string | kcat
string | Unit_Kcat
string | km_kcat
string | Unit_Kcat/Km
string | Kcleav
string | Unit_Kcleav
string | Commentary[Temp]
string | Commentary[pH]
string | Commentary[Mutant]
string | Commentary[Others]
string | pubmed_id
string | Source
string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
End of preview.
🚩Citation
Please cite the following paper if you use jackkuo/LLM-Enzyme-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}
}
- Downloads last month
- 111