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$begingroup$
I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if anyone know of the largest molecule datasets available. I will be testing ZINC, which has up to 38 atoms. Anyone knows of a larger dataset available?? Thanks!
quantum-chemistry computational-chemistry databases
asked 9 hours ago
BladeBlade
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add a comment |
$begingroup$
I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if anyone know of the largest molecule datasets available. I will be testing ZINC, which has up to 38 atoms. Anyone knows of a larger dataset available?? Thanks!
quantum-chemistry computational-chemistry databases
asked 9 hours ago
BladeBlade
62 bronze badges
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
$endgroup$
$begingroup$
In retrospect -- after giving providing an answer (molecules encoded as SMILES), while «user1271772» provided an other answer about molecules keeping geometries, does your question for a larger data set refer to a dataset containing molecules larger than 38 atoms, or a dataset with more molecules than ZINC?
$endgroup$
– Buttonwood
5 hours ago
$begingroup$
Larger than 38 atoms. I was gonna say, but I appreciated your detail answer very much
$endgroup$
– Blade
5 hours ago
add a comment |
$begingroup$
I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if anyone know of the largest molecule datasets available. I will be testing ZINC, which has up to 38 atoms. Anyone knows of a larger dataset available?? Thanks!
quantum-chemistry computational-chemistry databases
asked 9 hours ago
BladeBlade
62 bronze badges
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
$endgroup$
I have been testing a machine learning approach for molecular energy prediction. The current dataset that I have is QM9, which is consist of molecules with up to 9 heavy atoms. I was wondering if anyone know of the largest molecule datasets available. I will be testing ZINC, which has up to 38 atoms. Anyone knows of a larger dataset available?? Thanks!
quantum-chemistry computational-chemistry databases
quantum-chemistry computational-chemistry databases
asked 9 hours ago
BladeBlade
62 bronze badges
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 9 hours ago
BladeBlade
62 bronze badges
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 9 hours ago
BladeBlade
62 bronze badges
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 9 hours ago
BladeBlade
62 bronze badges
asked 9 hours ago
BladeBlade
62 bronze badges
62 bronze badges
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Blade is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
$begingroup$
In retrospect -- after giving providing an answer (molecules encoded as SMILES), while «user1271772» provided an other answer about molecules keeping geometries, does your question for a larger data set refer to a dataset containing molecules larger than 38 atoms, or a dataset with more molecules than ZINC?
$endgroup$
– Buttonwood
5 hours ago
$begingroup$
Larger than 38 atoms. I was gonna say, but I appreciated your detail answer very much
$endgroup$
– Blade
5 hours ago
add a comment |
$begingroup$
In retrospect -- after giving providing an answer (molecules encoded as SMILES), while «user1271772» provided an other answer about molecules keeping geometries, does your question for a larger data set refer to a dataset containing molecules larger than 38 atoms, or a dataset with more molecules than ZINC?
$endgroup$
– Buttonwood
5 hours ago
$begingroup$
Larger than 38 atoms. I was gonna say, but I appreciated your detail answer very much
$endgroup$
– Blade
5 hours ago
$begingroup$
In retrospect -- after giving providing an answer (molecules encoded as SMILES), while «user1271772» provided an other answer about molecules keeping geometries, does your question for a larger data set refer to a dataset containing molecules larger than 38 atoms, or a dataset with more molecules than ZINC?
$endgroup$
– Buttonwood
5 hours ago
$begingroup$
In retrospect -- after giving providing an answer (molecules encoded as SMILES), while «user1271772» provided an other answer about molecules keeping geometries, does your question for a larger data set refer to a dataset containing molecules larger than 38 atoms, or a dataset with more molecules than ZINC?
$endgroup$
– Buttonwood
5 hours ago
$begingroup$
Larger than 38 atoms. I was gonna say, but I appreciated your detail answer very much
$endgroup$
– Blade
5 hours ago
$begingroup$
Larger than 38 atoms. I was gonna say, but I appreciated your detail answer very much
$endgroup$
– Blade
5 hours ago
add a comment |
2 Answers
2
active
oldest
votes
$begingroup$
The ISOL24 database (http://www.thch.uni-bonn.de/tc.old/downloads/GMTKN/GMTKN55/ISOL24.html) contains molecules with up to 81 atoms!
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
$endgroup$
add a comment |
$begingroup$
This sounds like you were exploring work at least related to the work by the Lilienfeld group equally hosting a dedicated site here about data sets already used in their earlier and ongoing exploration of chemical space, programs used to work with the data, and publications.
To go considerably higher in molecule count than QM9, you could either go for
GDB-11 about small organic molecules up to 11 atoms of C, N, O and F which «contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds», described in J. Chem. Inf. Model. 2007, 47, 342-353 (doi.org/10.1021/ci600423u), or
GDB-13, about «small organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules. With 977 468 314 structures, GDB-13 is the largest publicly available small organic molecule database to date». This one was described in J. Am. Chem. Soc. 2009, 131, 8732-8733 (doi.org/10.1021/ja902302h)
Convienently, you can download both -- including sub-sets like «containing only carbon and nitrogen», or «chlorine and sulfur», or «fragrance like» in case you don't want to fetch 2GB of already compressed data -- from the Reymond group. To quote: «All the molecules are stored in dearomatized, canonized SMILES format.»
The even larger GDB-17 («of up to 17 atoms of C, N, O, S, and halogens» with an universe of 166 billion entries, described in J. Chem. Inf. Model. 2012, 52, 2864-2875, [doi.org/10.1021/ci300415d, open access]) is accessible to the public on this site as a 50 million random subset only, partly because the gzipped archive is about 400GByte. Among the publications citing this work is for example the Lilienfeld group again for machine learning (J. Chem. Phys. 143, 084111 (2015), doi.org/10.1063/1.4928757).
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
$endgroup$
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
add a comment |
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2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
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votes
$begingroup$
The ISOL24 database (http://www.thch.uni-bonn.de/tc.old/downloads/GMTKN/GMTKN55/ISOL24.html) contains molecules with up to 81 atoms!
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
$endgroup$
add a comment |
$begingroup$
The ISOL24 database (http://www.thch.uni-bonn.de/tc.old/downloads/GMTKN/GMTKN55/ISOL24.html) contains molecules with up to 81 atoms!
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
$endgroup$
add a comment |
$begingroup$
The ISOL24 database (http://www.thch.uni-bonn.de/tc.old/downloads/GMTKN/GMTKN55/ISOL24.html) contains molecules with up to 81 atoms!
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
$endgroup$
The ISOL24 database (http://www.thch.uni-bonn.de/tc.old/downloads/GMTKN/GMTKN55/ISOL24.html) contains molecules with up to 81 atoms!
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
edited 1 hour ago
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
answered 6 hours ago
user1271772user1271772
5884 silver badges13 bronze badges
5884 silver badges13 bronze badges
add a comment |
add a comment |
$begingroup$
This sounds like you were exploring work at least related to the work by the Lilienfeld group equally hosting a dedicated site here about data sets already used in their earlier and ongoing exploration of chemical space, programs used to work with the data, and publications.
To go considerably higher in molecule count than QM9, you could either go for
GDB-11 about small organic molecules up to 11 atoms of C, N, O and F which «contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds», described in J. Chem. Inf. Model. 2007, 47, 342-353 (doi.org/10.1021/ci600423u), or
GDB-13, about «small organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules. With 977 468 314 structures, GDB-13 is the largest publicly available small organic molecule database to date». This one was described in J. Am. Chem. Soc. 2009, 131, 8732-8733 (doi.org/10.1021/ja902302h)
Convienently, you can download both -- including sub-sets like «containing only carbon and nitrogen», or «chlorine and sulfur», or «fragrance like» in case you don't want to fetch 2GB of already compressed data -- from the Reymond group. To quote: «All the molecules are stored in dearomatized, canonized SMILES format.»
The even larger GDB-17 («of up to 17 atoms of C, N, O, S, and halogens» with an universe of 166 billion entries, described in J. Chem. Inf. Model. 2012, 52, 2864-2875, [doi.org/10.1021/ci300415d, open access]) is accessible to the public on this site as a 50 million random subset only, partly because the gzipped archive is about 400GByte. Among the publications citing this work is for example the Lilienfeld group again for machine learning (J. Chem. Phys. 143, 084111 (2015), doi.org/10.1063/1.4928757).
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
$endgroup$
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
add a comment |
$begingroup$
This sounds like you were exploring work at least related to the work by the Lilienfeld group equally hosting a dedicated site here about data sets already used in their earlier and ongoing exploration of chemical space, programs used to work with the data, and publications.
To go considerably higher in molecule count than QM9, you could either go for
GDB-11 about small organic molecules up to 11 atoms of C, N, O and F which «contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds», described in J. Chem. Inf. Model. 2007, 47, 342-353 (doi.org/10.1021/ci600423u), or
GDB-13, about «small organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules. With 977 468 314 structures, GDB-13 is the largest publicly available small organic molecule database to date». This one was described in J. Am. Chem. Soc. 2009, 131, 8732-8733 (doi.org/10.1021/ja902302h)
Convienently, you can download both -- including sub-sets like «containing only carbon and nitrogen», or «chlorine and sulfur», or «fragrance like» in case you don't want to fetch 2GB of already compressed data -- from the Reymond group. To quote: «All the molecules are stored in dearomatized, canonized SMILES format.»
The even larger GDB-17 («of up to 17 atoms of C, N, O, S, and halogens» with an universe of 166 billion entries, described in J. Chem. Inf. Model. 2012, 52, 2864-2875, [doi.org/10.1021/ci300415d, open access]) is accessible to the public on this site as a 50 million random subset only, partly because the gzipped archive is about 400GByte. Among the publications citing this work is for example the Lilienfeld group again for machine learning (J. Chem. Phys. 143, 084111 (2015), doi.org/10.1063/1.4928757).
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
$endgroup$
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
add a comment |
$begingroup$
This sounds like you were exploring work at least related to the work by the Lilienfeld group equally hosting a dedicated site here about data sets already used in their earlier and ongoing exploration of chemical space, programs used to work with the data, and publications.
To go considerably higher in molecule count than QM9, you could either go for
GDB-11 about small organic molecules up to 11 atoms of C, N, O and F which «contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds», described in J. Chem. Inf. Model. 2007, 47, 342-353 (doi.org/10.1021/ci600423u), or
GDB-13, about «small organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules. With 977 468 314 structures, GDB-13 is the largest publicly available small organic molecule database to date». This one was described in J. Am. Chem. Soc. 2009, 131, 8732-8733 (doi.org/10.1021/ja902302h)
Convienently, you can download both -- including sub-sets like «containing only carbon and nitrogen», or «chlorine and sulfur», or «fragrance like» in case you don't want to fetch 2GB of already compressed data -- from the Reymond group. To quote: «All the molecules are stored in dearomatized, canonized SMILES format.»
The even larger GDB-17 («of up to 17 atoms of C, N, O, S, and halogens» with an universe of 166 billion entries, described in J. Chem. Inf. Model. 2012, 52, 2864-2875, [doi.org/10.1021/ci300415d, open access]) is accessible to the public on this site as a 50 million random subset only, partly because the gzipped archive is about 400GByte. Among the publications citing this work is for example the Lilienfeld group again for machine learning (J. Chem. Phys. 143, 084111 (2015), doi.org/10.1063/1.4928757).
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
$endgroup$
This sounds like you were exploring work at least related to the work by the Lilienfeld group equally hosting a dedicated site here about data sets already used in their earlier and ongoing exploration of chemical space, programs used to work with the data, and publications.
To go considerably higher in molecule count than QM9, you could either go for
GDB-11 about small organic molecules up to 11 atoms of C, N, O and F which «contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple bonds», described in J. Chem. Inf. Model. 2007, 47, 342-353 (doi.org/10.1021/ci600423u), or
GDB-13, about «small organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules. With 977 468 314 structures, GDB-13 is the largest publicly available small organic molecule database to date». This one was described in J. Am. Chem. Soc. 2009, 131, 8732-8733 (doi.org/10.1021/ja902302h)
Convienently, you can download both -- including sub-sets like «containing only carbon and nitrogen», or «chlorine and sulfur», or «fragrance like» in case you don't want to fetch 2GB of already compressed data -- from the Reymond group. To quote: «All the molecules are stored in dearomatized, canonized SMILES format.»
The even larger GDB-17 («of up to 17 atoms of C, N, O, S, and halogens» with an universe of 166 billion entries, described in J. Chem. Inf. Model. 2012, 52, 2864-2875, [doi.org/10.1021/ci300415d, open access]) is accessible to the public on this site as a 50 million random subset only, partly because the gzipped archive is about 400GByte. Among the publications citing this work is for example the Lilienfeld group again for machine learning (J. Chem. Phys. 143, 084111 (2015), doi.org/10.1063/1.4928757).
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
answered 5 hours ago
ButtonwoodButtonwood
10.9k1 gold badge22 silver badges47 bronze badges
10.9k1 gold badge22 silver badges47 bronze badges
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
add a comment |
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
I don't think any of these have more than 81 atoms!
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
$begingroup$
Ok I see the confusion. @Buttonwood perhaps you can answer this question: chemistry.stackexchange.com/questions/119804/…
$endgroup$
– user1271772
4 hours ago
add a comment |
Blade is a new contributor. Be nice, and check out our Code of Conduct.
Blade is a new contributor. Be nice, and check out our Code of Conduct.
Blade is a new contributor. Be nice, and check out our Code of Conduct.
Blade is a new contributor. Be nice, and check out our Code of Conduct.
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$begingroup$
In retrospect -- after giving providing an answer (molecules encoded as SMILES), while «user1271772» provided an other answer about molecules keeping geometries, does your question for a larger data set refer to a dataset containing molecules larger than 38 atoms, or a dataset with more molecules than ZINC?
$endgroup$
– Buttonwood
5 hours ago
$begingroup$
Larger than 38 atoms. I was gonna say, but I appreciated your detail answer very much
$endgroup$
– Blade
5 hours ago