Descriptor whole molecule

Murcko frameworks allow for an abstract molecular representation, whereby the side chains of the structure are trimmed, preserving only the rings and the linkers that connect rings. An RDKit script was used in order to generate customized Murcko frameworks. Here, atom and bond types are preserved. The resulting Murcko framework descriptor was represented by a valid SMILES string. 

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Besides these LFER-based models, approaches have been developed using whole-molecule descriptors and learning algorithms other then multiple linear regression (see Section 10.1.2). 

Other whole molecule descriptors that do not require alignment include the Weighted Holistic Invariant Molecular (WHIM) indices developed by Todeschini et al. [70]. These indices are calculated from the 3D coordinates, which are weighted and centered to make them invariant to translation principal component analysis (PCA) is applied to obtain three principal components. These are used to produce new coordinates, which can be analyzed to obtain a series of 10 descriptors based on eigenvalues and the third-order and fourth-order moments of the three score column vectors. These descriptors are related to molecular size, shape, symmetry, and atom distribution and density. 

Katritzky AR, Fara DC, Petrukhin R, Tatham DB, Maran U, Lomaka A, Karelson M. The present utility and future potential for medicinal chemistry of QSAR/QSPR with whole molecule descriptors. Curr Top Med Chem 2002 2 1333-1356. 

APPENDIX LIST OF PRECLAV WHOLE MOLECULE DESCRIPTORS... 

A broad variety of electronic whole molecule descriptors have been used to encode electronic features in QSAR... 

Site-specific reactivity indices are arrived at by considering electronic information at specific locations in the molecule. The electrophilic and nucleophilic superdelocalizabilities at atom i are energy-weighted atomic electron densities. The electrophilic superdelocalizability roughly measures the availability of electrons at atom i nucleophilic superdelocalizability measures the availability of room on atom i for additional electron density. While these indices are atomic in nature, they may be classified as whole molecule descriptors if atom i is a fixed position in a series of congeners, or if the maximum superdelocalizability among all the atoms is chosen. 

If one considers only the electron densities in the highest occupied and lowest unoccupied MOs, the so-called electrophilic and nucleophilic frontier orbital densities result. These descriptors suppose that the HOMO and LUMO are far more important than the other MOs in determining the position and likelihood of electrophilic or nucleophilic attack. Again, when used in the manner discussed previously, these atom-specific indices become whole molecule descriptors. 

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