Contents: General Information Property Distributions Clustering and Diversity Downloads
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Catalog Version | Catalog Count | Num. Filtered | Free | Purchasable | Pubchem | Depleted |
---|---|---|---|---|---|---|
2015-04-17 | 198774 | 17193 | Yes (1) | Yes (1) | No | No |
"Usual" Subset Downloads: mol2 | SDF | Flexibase | more…
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We sort the ligands by molecular weight as a proxy for complexity. We then use the algorithm of Bienfait to incrementally select compounds that differ from all previous by the given Tanimoto cutoff. This is a very cheap clustering technique that scales well with set size and gives some indication of the amount of chemical redundancy in the dataset at various Tanimoto levels. N/A indicates that clustering is pending.
All | 269386 |
90% | 80983 |
80% | 35431 |
70% | 15917 |
60% | 6587 |
Molecules are available in four formats: isomeric SMILES, mol2,
SDF and flexibase. Molecules are represented as a single pH=7 form.
Additional representations (protonation variants and tautomers) are
available in three incremental subsets to augment the single
representative: medium pH (5.75 to 8.25), high pH 7.0-9.5
(e.g. for docking to metals), and low pH 4.5-7.0 (e.g. for docking
to a positively charged binding site).
Larger files are broken up into slices to faciliate downloading.
You may download individual slices or use c-shell scripts to download
a single representation (pH 7.0),
all Usual ligands (pH 5.75 to 8.25), ligands for metals (5.75-9.5) or All.
Note that these sets are overlapping so you do not want to download
both Metals and All.
We expect dockers will want to just download the "Usual" subset. Chemical informaticists who require only a single form of each molecule may want just the "Single" representation. If files appear to be missing or incomplete, please try again tomorrow as the export may still be in progress. If problems persist for 48 hours please complain to comments at docking dot org
File format | Individual slices | Scripts to download slices | |||
---|---|---|---|---|---|
SMILES | Reference | mid pH | high pH | low pH | |
mol2 | 0 1 2 | 0 | 0 | 0 | Single Usual Metals All |
SDF | 0 1 2 | 0 | 0 | 0 | Single Usual Metals All |
Flexibase | Single Usual Metals All |