Similarity atom mapping

Table 4.29 summarizes the metrics for 4 plans to the antibiotic thienamycin and Figure 4.62 shows the corresponding synthesis map with starting materials used. The two Melillo and Reider variants by Merck co-workers are the better performers however each plan has certain attributes that are not found in the other. The slightly shorter Reider plan has a higher overall reaction yield though it has a similar atom economy and overall kernel RME to the Melillo plan. Further optimization would be required to result in all optimum metrics occurring in the same plan. 

One individual of a population represents a possible superimposition of the molecules under consideration. The chromosomes code the atoms of the different structures, which are mapped onto each other (match list) on the basis of either identical atom types or similar atomic properties (e.g., partial atomic charges) within a given range. The molecules are treated conformationally flexible during superimpo-... 

Another application of anomalous dispersion and SR is the case of a protein containing a cofactor of two metal atoms of similar atomic number. In such a case the native electron density map would not clearly indicate which metal atom is which. However, the anomalous dispersion /" values could be made markedly different by suitable choice... 

While STM gave researchers the abifity to probe atomic scale events at metal and semiconducting surfaces, many of the materials of interest to surface scientists fall outside these classes of materials, such as the surfaces of oxides and biological materials that lack conductivity. AFM is a tool that provides similar surface mapping of materials as STM, but can be used for systems that are nonconductive as well. 

The atom-mapping method provides a quantitative measure of the similarity between a pair of 3D molecules, A and B, that are represented by their interatomic distance matrices. The measure is calculated in two stages. First, the geometric environment of each atom in A is compared with the corresponding environment of each atom in B to determine the similarity between each possible pair of atoms. The resulting interatomic similarities are then used to identify pairs of geometrically related atoms, and these equivalences allow the calculation of the overall intermolecular similarity. 

The description above has assumed that the property that is stored at the vertices of the tessellated icosahedron describing a molecule is either the minimal or the radial distance to the molecular surface. However, it is equally possible to store at each vertex any sort of property that can be calculated for that point in 3D space, such as the molecular electrostatic potential. Thus SPERM, like atom-mapping, allows local, property-based 3D similarity searching. 

C. A. Pepperrell, P. Willett, and R. Taylor, Tetrahedron Comput. MethodoL, 3,575 (1990). Implementation and Use of an Atom-Mapping Procedure for Similarity Searching in Databases of 3-D Chemical Structures. 

D. J. Wild and P, Willett,/. Chem. Inf. Comput. Sci., 34,224 (1994). Similarity Searching in Files of Three-Dimensional Chemical Structures Implementation of Atom Mapping on the Distributed Array Processor DAP-610, the MasPar MP-1104 and the Connection Machine CM-200. 

The developers of CASREACT have pubhshed methods of assigning and searching both reaction centres and explicit reaction schemes. At the time of writing its user interface does not allow the assignment of atom mappings or reaction centres. CASREACT also can retrieve false hits where the direction of the arrow is reversed, similar to the limitation in ChemBase. Improvements in its user interface may resolve some of these limitations. 

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