Shape similarity method

Another successful application of a shape similarity method was reported by Cramer et al. (83). Over 400 compounds were synthesized and tested for their inhibition of angiotensin II. The... 

Ebalunode, J. O., Zheng, W. (2009) Unconventional 2D shape similarity method affords comparable enrichment as a 3D shape method in virtual screening experiments. J Chem Inf Model 49, 1313-1320. 

The field of synthetic enzyme models encompasses attempts to prepare enzymelike functional macromolecules by chemical synthesis [30]. One particularly relevant approach to such enzyme mimics concerns dendrimers, which are treelike synthetic macromolecules with a globular shape similar to a folded protein, and useful in a range of applications including catalysis [31]. Peptide dendrimers, which, like proteins, are composed of amino acids, are particularly well suited as mimics for proteins and enzymes [32]. These dendrimers can be prepared using combinatorial chemistry methods on solid support [33], similar to those used in the context of catalyst and ligand discovery programs in chemistry [34]. Peptide dendrimers used multivalency effects at the dendrimer surface to trigger cooperativity between amino acids, as has been observed in various esterase enzyme models [35]. 

Andrews KM, Cramer RD. Toward general methods of targeted library design topomer shape similarity searching with diverse structures as queries. / Med Chem 2000 43 1723-40. 

The latter method, the template method, involves a reaction to produce a transition state similar to the desired product using a template. The template should have a shape similar to the space of the product. The template interacts with the substrate by forming noncovalent bonds such as coordination bonds (Fig. 3). The representative and most successful examples are found in crown ether chemistry. In the chemistry, alkali metals act as templates to create a crown-ether-like transition state with an ethylene glycol substrate by using metal-oxygen coordination bonds. 

Mezey, P.G. (1995) Methods of molecular shape-similarity analysis and topological shape design. 

Gaussian Shape Similarity by Good and Richards. This method introduced the use of Gaussians for molecular shape matching for... 

The basic idea of alignment-free shape matching is that a set of rotation- and translation-free descriptors are calculated for con-formers under consideration, and then some similarity measure is devised to quantify the similarity between two molecular objects. Zauhar s shape signatures (45), Breneman s PEST and PESD methods (54-56), the USR (ultrafast shape recognition) method... 

The USR (Ultrafast Shape Recognition) Method. This method was reported by Ballester and Richards (53) for compound database search on the basis of molecular shape similarity. It was reportedly capable of screening billions of compounds for similar shapes on a single computer. The method is based on the notion that the relative position of the atoms in a molecule is completely determined by inter-atomic distances. Instead of using all inter-atomic distances, USR uses a subset of distances, reducing the computational costs. Specifically, the distances between all atoms of a molecule to each of four strategic points are calculated. Each set of distances forms a distribution, and the three moments (mean, variance, and skewness) of the four distributions are calculated. Thus, for each molecule, 12 USR descriptors are calculated. The inverse of the translated and scaled Manhattan distance between two shape descriptors is used to measure the similarity between the two molecules. A value of 1 corresponds to maximum similarity and a value of 0 corresponds to minimum similarity. 

The existence of the surface contribution to the effective magnetostriction of nanocrystalline alloys has been confirmed theoretically in terms of the dipolar model (Szumiata et al. 1999). These authors showed that, due to the limited radius of the nanoparticles, additional magnetostrictive stresses are localised at the interfaces. The evaluation of the influence of the dipolar interaction on the magnetostriction in crystalline grains of perfect spherical shape surrounded by a magnetic environment of about 0.S nm with either crystalline or amorphous structure has been calculated. A similar method was previously used to obtain the surface and volume anisotropy (Draaisma and de Jonge 1988) and to... 

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