Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 PubChemSimilaritySearch

Source Notebook

Search the PubChem database for similar compounds

Contributed by: Jason Biggs

ResourceFunction["PubChemSimilaritySearch"][mol]

returns a list of "PubChemCompoundID" identifiers for compounds similar to the molecule or chemical entity mol.

ResourceFunction["PubChemSimilaritySearch"][mol,"Molecule"]

returns a list of Molecule objects constructed from the external identifiers similar to mol.

Details and Options

ResourceFunction["PubChemSimilaritySearch"] uses the "PubChem" service connection to query the PubChem database.
PubChemSimilaritySearch takes an option "SearchType". Possible settings for this option include:
"Similarity2DSearch"Tanimoto similarity of topological fingerprints
"Similarity3DSearch"Tanimoto similarity of 3D shape fingerprints
"Original"exact match to input
"Parent"parent compound
"SameStereo"same stereo
"SameIsotopes"same isotopes
"SameConnectivity"same connectivity
"SameFormula"same molecular formula
"SameTautomer"same tautomer
"SameParent"same parent
"SameParentStereo"same parent stereo
"SameParentIsotopes"same parent isotopes
"SameParentConnectivity"same parent connectivity
"SameParentTautomer"same parent tautomer
When using either the search type "Similarity2DSearch" or "Similarity3DSearch", the option "TanimotoThreshold" can be used to control the minimum similarity score for results.

Examples

Basic Examples (5) 

Find the compound ID for a similar molecules:

In[1]:=
ResourceFunction["PubChemSimilaritySearch"][ Entity["Chemical", "TrichloroacetylChloride"]]
Out[1]=

Perform the same search, but return the results as Molecule objects:

In[2]:=
ResourceFunction["PubChemSimilaritySearch"][ Entity["Chemical", "TrichloroacetylChloride"], "Molecule"]
Out[2]=

Visualize the results using MoleculePlot:

In[3]:=
GraphicsColumn[{MoleculePlot@First@%, GraphicsRow[MoleculePlot /@ Rest[%]]}]
Out[3]=

Search PubChem for tautomers:

In[4]:=
(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/9a4428cd-ea41-47a7-860e-a16a9366c3e5"]
Out[4]=

Get a list of molecules with the same connectivity as adenosine:

In[5]:=
(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/95babadb-167b-45b8-bfe7-cf89d2ef832b"]
Out[5]=

Visualize the molecules using MoleculePlot:

In[6]:=
GraphicsRow[MoleculePlot /@ %]
Out[6]=

Get a list of IDs for compounds with the same parent:

In[7]:=
ResourceFunction["PubChemSimilaritySearch"][ Molecule["O[C@H](c1cc(nc2c1cccc2C(F)(F)F)C(F)(F)F)[C@H]1CCCCN1"], "SearchType" -> "SameParent"]
Out[7]=

Get a list of isomers by using the "SameFormula" search type:

In[8]:=
(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/0a669263-c091-49a9-8062-6aa34081dbbf"]
Out[8]=

Scope (2) 

PubChemSimilaritySearch can be used with Entity or Molecule objects:

In[9]:=
ResourceFunction["PubChemSimilaritySearch"][#, "SearchType" -> "Original"] & /@ {Molecule["caffeine"], Entity["Chemical", "Caffeine"]}
Out[9]=

PubChemSimilaritySearch will automatically thread over lists:

In[10]:=
mols = Molecule /@ {"CCCCCCCNC(=O)CCNC(=O)[C@@H](C(CO)(C)C)O", "O=C1CC[C@]2(C(=C1)CC[C@@H]1[C@@H]2[C@@H](O)C[C@]2([C@H]1CC[C@]2(O)C(=O)COS(=O)(=O)C)C)C", "CCCP(C1(C)CCC1)C", "SC1CC1", "COC(=O)c1cccnc1", "O=C1CC[C@@H]2[C@]1(C)CC[C@H]1[C@H]2CCc2c1ccc(c2)OS(=O)(=O)N", "CC[C@@H](C(=O)O[C@@H]1CC(C)(C)C[C@H]2[C@]1(CC[C@@]1(C2=CC[C@H]2[C@@]1(C)CC[C@@H]1[C@]2(C)CCC(=O)C1(C)C)C)C(=O)O)C", "CC[C@H](N[C@H]1CC[C@@H]1C)C", "CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@@H]2O[C@@H](C)[C@@H]([C@](C2)(C)OC)O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@](C[C@H](CN([C@@H]([C@H]([C@]1(C)O)O)C)C)C)(C)O", "CCOc1nc(N)nc2c1ncn2[C@@H]1C[C@@H]([C@H](O1)CO)O"}; Length@ResourceFunction["PubChemSimilaritySearch"][mols]
Out[11]=

Options (2) 

By adjusting the Tanimoto threshold, the number of similar compounds returned can be controlled:

In[12]:=
mol = Molecule[ "CCOC(=O)C1=C(C)NC(=C([C@@H]1c1c(F)c(F)c(c(c1F)F)F)C(=O)OCC)C"]; similarityData = ResourceFunction[ "DynamicMap"][{#, Length@ResourceFunction["PubChemSimilaritySearch"][mol, "TanimotoThreshold" -> #]} &, Join[Range[60, 90, 10], Range[91, 99]]]
Out[12]=

Use ListLogPlot to visualize the relationship between threshold and the size of the similarity space:

In[13]:=
ListLogPlot[ similarityData, AxesLabel -> {"threshold", "# of compounds"}]
Out[13]=

Publisher

JasonB

Version History

  • 1.0.0 – 09 April 2020

Source Metadata

  • Citation:
    • Kim, S. et al., "PubChem 2019 update: improved access to chemical data." Nucleic Acids Research, vol. 47, no. D1, D1102–D1109, 2019. DOI: 10.1093/nar/gky1033

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