Datasets:
jackkuo
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LLM-Ribozyme-Kinetics-Golden-Benchmark

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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