Geometric atom-pair descriptors

Sheridan, R.P., Miller, M.D., Underwood, D.J., and Kearsley, S.K. Chemical similarity using geometric atom pair descriptors. /. Chem. Inf. Comput. Sci. 1996, 36, 128-136. 

Using the geometric distance in place of the topological distance between any pair of atom types, geometric atom pair descriptors were analogously defined [Sheridan, Nilakantan et al, 1989 Sheridan, Miller et al, 1996]. Atom types are defined here by the chemical element, number of heavy-atom cormections, number of n electron pairs, number of attached hydrogens, and formal charge. 

Kearsley SK, Sallamack S, Fluder EM, Andose JD, Mosley RT, Sheridan RP (1996) Chemical similarity using physicochemical property descriptors. J Chem Inf Comput Sci 36 11-127 Sheridan RP, Miller MD, Underwood DJ, Kearsley SK (1996) Chemical similarity using geometric atom pair descriptors. J Chem Inf Comput Sci 36 128-136 Hert J, Willett P, Wilton DJ, Acklin P, Azzaoui K, Jacoby E, Schuffenhauer A (2004) Comparison of FP-based for virtual screening using multiple bioactive structures. J Chem Inf Comput Sci 44 1177-1185... 

The summation in Formnla (4.24) can be calculated for all atom pairs or only for all pairs of bonded atoms. The gravitational index is a measure of the spatial distribution of masses in the molecule and is similar to the geometrical principal moments of the inertia descriptor. An electronic index leie is calcnlated with a similar formula... 

Other simple geometrical descriptors are interatomic distances between pairs of atoms s and t. Interatomic distances are devided into intramolecular interatomic distances, i.e. distances between any pair of atoms (s, t) within the molecule, and intermo-lecular interatomic distances, i.e. distances between atoms of a molecule and atoms of a receptor structure, a reference compound or another molecule. While classical computational chemistry describes molecular geometry in terms of three-dimensional Cartesian coordinates or internal coordinates, the -> distance geometry (DG) method takes the interatomic distances as the fundamental coordinates of molecules, exploiting their close relationship to experimental quantities and molecular energies. 

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