Topology-based similarity

Basak and Grunwald" also used topologically based similarity for KNN estimation of the mutagenicity of a set of 95 aromatic amines and the boiling point of a group of over 2900 chemicals with good results. 

A bioisostere is a compound resulting from the exchange of an atom or of a group of atoms with another, broadly similar, atom or group of atoms. The objective of a bioisosteric replacement is to create a new compound presenting similar biological properties to the parent compound. The bioisosteric replacement may be physicochemically or topologically based (IUPAC). 

Fig. 6 Four nearest neighbors (analogs) for a heteroaromatic probe compound selected from a principle component-based similarity space, a topological index-based similarity space, and a tailored topological index space, respectively...

ADMA = adjustable density matrix assembler AFDF = additive fiizzy density fragmentation GSTE = geometrical similarity as topological equivalence MEDLA = molecular electron density loge assembler MEP = molecular electrostatic potential RBSM = resolution-based similarity measures SGM = shape group methods VDWS = van der Waals surface ID, 2D, 3D = one, two, and three dimensions. 

Resolution-based similarity measures Similarity expressed by the geometrical or topological resolution required to distinguish objects. 

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