Alignment rules molecular similarity

Molecular docking and structural alignment methods are based on three-dimensional structures of candidate molecules that can be generated by rule-based methods such as CORINA [13, 14] or CONCORD [15]. However, methods based on three-dimensional structures are computationally quite demanding and cannot routinely be applied to databases of hundreds of thousands of compounds today. For this reason, a number of fast methods to determine molecular similarity have been developed that operate solely on connectivity and atom types of molecules. Such tools allow rapid prescreening of very large databases and avoid a conformational analysis of each candidate molecule. 

Constructs 3D structures from SMILES notation using a library of fragments and rules. ASP for molecular similarity comparisons, CONSTRICTOR for distance geometry, and CAMELEON for protein sequence alignment. NEMESIS for desktop molecular modeling on the Mac-II and IBM PC. 

Additional information on electronic structure may be obtained from the x-ray emission spectra of the SiOj polymorphs. As explained in Chapter 2, x-ray emission spectra obey rather strict selection rules, and their intensities can therefore give information on the symmetry (atomic or molecular) of the valence states involved in the transition. In order to draw a correspondence between the various x-ray emission spectra and the photoelectron spectrum, the binding energies of core orbitals must be measured. In Fig. 4.12 (Fischer et al., 1977), the x-ray photoelectron and x-ray emission spectra of a-quartz are aligned on a common energy scale. All three x-ray emission spectra may be readily interpreted within the SiO/ cluster model. Indeed, the Si x-ray emission spectra of silicates are all similar to those of SiOj, no matter what their degree of polymerization. Some differences in detail exist between the spectra of a-quartz and other well-studied silicates, such as olivine, and such differences will be discussed later. 

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