Can anyone point me into the right direction as to the protocols that is needed to create a (1) Molecular Similarity plot of the chemical space and a (2) Molecular Similarity plot of the biological space.
I am aware that we could either use fingerprints or molecular descriptors to describe the physicochemical properties of the compounds, what steps would be next? (besides using these descriptors as input to PCA or Self-Organizing Maps).
Any comments or suggestions is greatly appreciated. :)
Joerg Kurt Wegner [ Editor ]
I personally like graphs, since they allow to mix chemical and biological spaces in any way. Here a chemical similarity visualization I created using OpenBabel, CytoScape (integrates yEd I mentioned in the article), and some Python scripting. Besides, CytoScape is a very nice tool for initial data exploration, since it allows filtering networks on multiple node and edge properties. In short, if you create a full similarity matrix and use an edge filtering (e.g. chemical similarity) between two nodes (e.g. chemical compounds) then you obtain automatically a graph clustering. This is providing a lot of insights and is something I really like for complex data sets. Expanding this with biological information should now be a piece of cake and please note the linking options of CytoScape for biological web-services.