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SMARTS Dataset

Smiles ARbitary Target Specification (SMARTS) is a language to formulate chemical patterns, such as substructures in molecules.[1] To evaluate algorithms to search for chemical patterns in molecules, we present a collection of SMARTS expressions extracted from various literature sources[2-13] and a collection of SMARTS-molecule pairs created from the ZINC database. Additionally, a test case with a highly symmetric SMARTS-SMILES pair and a subset of the ZINC Lead-Like database is provided.

If you use this set or any subset, please cite

  • Ehrlich, H. C.; Rarey, M. Systematic Benchmark of Substructure Search in Molecular Graphs - From Ullmann to VF2. J Cheminform 2012, 4 (1), 13. DOI: https://doi.org/10.1186/1758-2946-4-13
  • and the original reference(s)

SMARTS Files

In the following, the literature references and download links to the files containing the corresponding SMARTS expressions are listed.

Note that the original publication by Baell and colleagues[12] contains patterns in SLN notation. A conversion into SMARTS was performed by Rajarshi Guha using CACTVS.[14]

Benchmark Sets

The following sets contain the literature-derived SMARTS files, various versions of a subset of the PAINS[12] SMARTS patterns, sets of SMARTS-SMILES pairs to evaluate the influence of substructure and molecule size on the algorithmic runtime, the first 100,000 molecules from the ZINC Lead-Like database[15] as of 12 February 2011 to represent a small database, and a phenyl ring-fullerene pair file as worst-case symmetry search case.

[1] Daylight Theory Manual. https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
[2] Hann, M.; Hudson, B.; Lewell, X.; Lifely, R.; Miller, L.; Ramsden, N. Strategic Pooling of Compounds for High-Throughput Screening. J Chem Inf Comput Sci 1999, 39 (5), 897-902. DOI: https://doi.org/10.1021/ci990423o
[3] Walters, W. P.; Murcko, M. A. Prediction of 'Drug-Likeness'. Adv Drug Deliv Rev 2002, 54 (3), 255-271. DOI: https://doi.org/10.1016/s0169-409x(02)00003-0
[4] Abolmaali, S. F.; Wegner, J. K.; Zell, A. The Compressed Feature Matrix - A Fast Method for Feature Based Substructure Search. J Mol Model 2003, 9 (4), 235-241. DOI: https://doi.org/10.1007/s00894-003-0126-0
[5] Olah, M.; Bologa, C.; Oprea, T. I. An Automated PLS Search for Biologically Relevant QSAR Descriptors. J Comput Aided Mol Des 2004, 18 (7-9), 437-449. DOI: https://doi.org/10.1007/s10822-004-4060-8
[6] Maass, P.; Schulz-Gasch, T.; Stahl, M.; Rarey, M. Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations. J Chem Inf Model 2007, 47 (2), 390-399. DOI: https://doi.org/10.1021/ci060094h
[7] Degen, J.; Wegscheid-Gerlach, C.; Zaliani, A.; Rarey, M. On the Art of Compiling and Using 'Drug-Like' Chemical Fragment Spaces. ChemMedChem 2008, 3 (10), 1503-1507. DOI: https://doi.org/10.1002/cmdc.200800178
[8] Ahmed, H. E.; Vogt, M.; Bajorath, J. Design and Evaluation of Bonded Atom Pair Descriptors. J Chem Inf Model 2010, 50 (4), 487-499. DOI: https://doi.org/10.1021/ci900512g
[9] Daylight SMARTS Examples. https://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html (last accessed May 25, 2010)
[10] Agrafiotis, D. K.; Gibbs, A. C.; Zhu, F.; Izrailev, S.; Martin, E. Conformational Sampling of Bioactive Molecules: A Comparative Study. J Chem Inf Model 2007, 47 (3), 1067-1086. DOI: https://doi.org/10.1021/ci6005454
[11] Enoch, S. J.; Madden, J. C.; Cronin, M. T. Identification of Mechanisms of Toxic Action for Skin Sensitisation Using a SMARTS Pattern Based Approach. SAR QSAR Environ Res 2008, 19 (5-6), 555-578. DOI: https://doi.org/10.1080/10629360802348985
[12] Baell, J. B.; Holloway, G. A. New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays. J Med Chem 2010, 53 (7), 2719-2740. DOI: https://doi.org/10.1021/jm901137j
[13] Kenny, P. W.; Montanari, C. A.; Prokopczyk, I. M. ClogP(alk): A Method for Predicting Alkane/Water Partition Coefficient. J Comput Aided Mol Des 2013, 27 (5), 389-402. DOI: https://doi.org/10.1007/s10822-013-9655-5
[14] Ihlenfeldt, W. D.; Takahashi, Y.; Abe, H.; Sasaki, S. Computation and Management of Chemical Properties in CACTVS: An Extensible Networked Approach toward Modularity and Compatibility. Journal of Chemical Information and Computer Sciences 2002, 34 (1), 109-116. DOI: https://doi.org/10.1021/ci00017a013
[15] ZINC Database. https://zinc.docking.org/