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SMSD specifications


Unique identifier OMICS_23663
Alternative name Small Molecule Subgraph Detector
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline asadrahman <>
  • person_outline Gemma L. Holliday <>
  • person_outline Janet Thornton <>
  • person_outline Matthew Bashton <>
  • person_outline Rainer Schrader <>

Publication for Small Molecule Subgraph Detector

SMSD in publications

PMCID: 5221824
PMID: 28068354
DOI: 10.1371/journal.pone.0168725

[…] to reaction thermodynamics, the structural similarity between two compounds is widely used to measure the diversity of the chemical space and analyze the metabolic networks [, , ]. for example, the smsd tool [] has been applied to compute the structural similarity between two compounds. in this article, we use smsd to compute the similarity scores between the input compounds and output […]

PMCID: 5122418
PMID: 27232942
DOI: 10.18632/oncotarget.9577

[…] that mirna pairs connected with the same small molecule had moderate target similarity (p = 0.1892). second, we employed the two-dimensional tanimoto chemical similarity score, which was measured by small molecule subgraph detector (smsd) software [], to evaluate the structural similarity between small molecules. the findings indicated that the small molecule pairs connecting with the same mirna […]

PMCID: 4764943
PMID: 26906215
DOI: 10.1038/srep21986

[…] metabolite mimetic nf-κb inhibitors. structural information on human metabolites of the kyoto encyclopedia of genes and genomes (kegg) were analyzed. structural comparisons were conducted using the small molecule subgraph detector. the results of structural similarity analysis of the 20 selected tom-derived compounds versus human metabolites are summarized in . results of extensive pairwise […]

PMCID: 4751976
PMID: 26585402
DOI: 10.1016/j.jmb.2015.11.010

[…] atoms forming the bond that is broken/formed in a reaction (). finally, the substrates and products of the reactions are compared using a common sub-graph detection algorithm implemented in smsd (small molecule subgraph detector) that identifies similar fragments from all the metabolites in a reaction ., a summary of the protocol used is provided in ., the csa stores information on catalytic […]

PMCID: 4402589
PMID: 25859612
DOI: 10.1186/1471-2105-16-S5-S11

[…] exact substructure (atom and bond types) of the larger structure being compared. the underlying cheminformatics functionality of biosmxpress is based on an open source java based toolkit called the small molecule subgraph detector (smsd) []. this toolkit is used to find the maximum common sub-graph between small molecules using atom type matches and bond sensitivity information. in addition […]

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SMSD institution(s)
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Zentrum fur Angewandte Informatik (ZAIK), Universitat zu Koln, Koln, Germany
SMSD funding source(s)
Supported as part of the mid-west Structural Genomic Consortium (SGC) by NIH grant (GM62414), US DOE under contract (W-31-109-ENG38), EMBL, Wellcome Trust, and IBM.

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