What does this tool do?
This tool computes the Euclidean distance between the Spectrophores™ descriptors of the target to each molecule stored in the library.
Spectrophores™ is a screening technology by Silicos which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows easy comparison of Spectrophores™ of different molecules.
Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar Spectrophores™. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations.
Advantages:
Hint: this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity.
Input
The target molecule must be a SD formatted file with the Spectrophores™ descriptors stored as metadata. Such files can be generated using the Compute physico-chemical properties tool.
Output
The library of compounds is a tabular file with one line per compound. One column contains the Spectrophores™ descriptors.
Cite
N M O'Boyle, C Morley and G R Hutchison - Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
Silicos - Spectrophores™ is a registered tool implemented in the open-source OpenBabel.