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SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This enables us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).


One of the possible MCS solutions between Isobutane and Cyclopropane

MCS search example Java code MCSSearch.java

Substructure search example Java code SubstructureSearch.java


Kindly support the SMSD by citing the following publication :

S. Asad Rahman, M. Bashton, G. L. Holliday, R. Schrader and J. M. Thornton: Small Molecule Subgraph Detector (SMSD) Toolkit, Journal of Cheminformatics 2009, 1:12 doi:10.1186/1758-2946-1-12

Download: Click here to download SMSD

The latest SMSD source code is available via github.



News (01.03.2013)
Note: BUILD on Java 1.7
  1. Fixed bond matcher for SP3 Nitrogen atom types.
  2. Optimised and cleaned few classes
  3. Complied using the latest CDK etc.


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