Similarity index?

I should like to compare two structures and quantify their similarity by various measures, starting with structural similarity. If I use the 3D alignment tool in Marvin Sketch, what do the numbers generated by the various options (extended atom types, pharmacophore types, MCS, and user defined atom pairs) mean? Are these Tanimoto coefficients or something else? In addition, how does one specify user defined atom pairs? Thank you.

 

Hi,

Indeed, similarity scores calculated by the 3D alignment tool are Tanimoto coefficients regardless of the options.

User defined atom pairs can be specified with the reaction arrow; select the reaction arrow from the toolbar on the right hand side of the marvin sketch window and the use the arrow to map atoms to each other. For further details you may wish to follow this link.

Does this help?

Regards,

Miklos