DD.chem.data: Drug-drug chemical similarities data

Description Usage Format Details Source References Examples

Description

Chemical structure similarities between 1253 FDA approved drugs obtained from DrugBank 3.0.

Usage

1

Format

A 1253 x 1253 named matrix where both rows and columns refer to DrugBank drugs. Drugs names are DrugBank 3.0 identifiers.

Details

This matrix contains the Tanimoto chemical structure similarity scores between 1253 DrugBank drugs. Canonical Simplified molecular-input line-entry specifications (SMILES) of the drugs were extracted from the DrugBank Drugcards. The SMILES were then converted into molecular extended fingerprints (1024 bits) using the rcdk package. The set of fingerprints was finally converted into a Tanimoto similarity matrix using the fp.sim.matrix rcdk function. All the real values contained in this matrix represent the chemical structure similarity between each possible pair of drugs and are comprised between 0 (completely different chimical structures) and 1 (identical chemical structures).

Source

The SMILES representations of the drugs were extracted by the Smiles_String_canonical fields of the DrugCards contained in the file drugbank.txt available at:

http://www.drugbank.ca/system/downloads/current/drugbank.txt.zip

References

Wishart, D., Knox, C., Guo, A., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., Woolsey, J.: DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34(Jan), D668-D672 (2006)

Guha, R.: Chemical Informatics Functionality in R. Journal of Statistical Software 18(6), (2007)

Examples

1
2

Example output

           DB00115    DB00116   DB00117    DB00118    DB00119   DB00120
DB00115 1.00000000 0.25192802 0.1231231 0.36828645 0.03728814 0.1262136
DB00116 0.25192802 1.00000000 0.1752137 0.21111111 0.05612245 0.2087379
DB00117 0.12312312 0.17521368 1.0000000 0.15357143 0.13253012 0.3877551
DB00118 0.36828645 0.21111111 0.1535714 1.00000000 0.04938272 0.1250000
DB00119 0.03728814 0.05612245 0.1325301 0.04938272 1.00000000 0.1929825
DB00120 0.12621359 0.20873786 0.3877551 0.12500000 0.19298246 1.0000000
DB00121 0.17948718 0.23046875 0.1609195 0.23469388 0.08943089 0.1733333
DB00122 0.04095563 0.06185567 0.1071429 0.03673469 0.25000000 0.1551724
DB00123 0.09933775 0.15346535 0.2903226 0.12851406 0.26829268 0.4029851
DB00125 0.11688312 0.20689655 0.2571429 0.13127413 0.20754717 0.3417722
           DB00121    DB00122    DB00123   DB00125
DB00115 0.17948718 0.04095563 0.09933775 0.1168831
DB00116 0.23046875 0.06185567 0.15346535 0.2068966
DB00117 0.16091954 0.10714286 0.29032258 0.2571429
DB00118 0.23469388 0.03673469 0.12851406 0.1312741
DB00119 0.08943089 0.25000000 0.26829268 0.2075472
DB00120 0.17333333 0.15517241 0.40298507 0.3417722
DB00121 1.00000000 0.08130081 0.25984252 0.2835821
DB00122 0.08130081 1.00000000 0.21428571 0.2115385
DB00123 0.25984252 0.21428571 1.00000000 0.5517241
DB00125 0.28358209 0.21153846 0.55172414 1.0000000

bionetdata documentation built on May 29, 2017, 7:55 p.m.