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Subset Summary

"all-clean" subset (# 16) - 16403865 entries

Contents: General Information   Property Distributions   Clustering and Diversity   Downloads

General Information

Search Criteria:
Created By: jji at cgl.ucsf.edu
Last Updated: 2013-12-18
Note: As Subset #6, but without 'yuck' compounds.

Flags
Nuisance Vernalis Asymmetric Atoms Asymmetric Double Bonds Alt. Nuisance
Yes No No No No

"Usual" Subset Downloads: mol2 | SDF | Flexibase | more…

Property Distributions

Clustering and Diversity

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.

All16403865
90%342803
80%40329
70%27726
60%7561

Downloads

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 slicesScripts to download slices
SMILES Reference   mid pH   high pH   low pH  
mol2 0 1 10 100 101 102 103 104 105 106 107 108 109 11 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 60 61 62 63 64 65 66 67 68 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9   0 1 10 11 12 13 14 15 16 2 3 4 5 6 7 8 9   0 1 10 11 12 13 2 3 4 5 6 7 8 9   Single Usual Metals All
SDF 0 1 10 100 101 102 103 104 105 106 107 108 109 11 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 60 61 62 63 64 65 66 67 68 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9   0 1 10 11 12 13 14 15 16 2 3 4 5 6 7 8 9   0 1 10 11 12 13 2 3 4 5 6 7 8 9   Single Usual Metals All
Flexibase  Single Usual Metals All
A product of BCIRC, the Bioinfomatics and Chemical Informatics Research Center @ UCSF. Last updated Aug 6, 2009. questions and discussion to zinc-fans at docking.org; bug reports to support at docking.org; any other correspondence to comments at docking.org. Terms of use. Privacy policy.