Shape matching

This approach of combining shape-matching and conformahonal analysis proved a useful complement to HTS. Some of the compounds identified by the computational screen were not detected in the original experimental screen. This was because their relative weak activity was difficult to separate from the noise of the assay. Nonetheless, these compounds had different scaffolds (i.e. were lead-hops ) compared to the previously known inhibitor. The key contribution from conformational analysis was that the newly discovered inhibitors were not found by the corresponding searches based on 2D methods. 

Most enzymes are very specific in their activity, and each chemical reaction in a living organism requires a specific enzyme. Their specificity arises from what is known as an active site, a location in the enzyme s molecule that has a shape matching that of a part of the molecule with which it reacts. The activity of the enzymes is affected by such factors as temperature and pH, each enzyme functioning best within a specific range of temperatures and pH. Outside this range the enzymes are structurally altered and their activity is either impaired or terminated. 

What molecular shapes match the arrangements of the bubbles in step 8 ... 

Rayleigh ellipsoids, arbitrarily normalized, are reproduced from Fig. 12.15. Spherical SiC particles match the circumstellar feature very poorly, but a wide distribution of shapes matches it quite well. This indicates that even shape information may sometimes be extracted from emission spectra of inaccessible particles. 

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... 

To employ the shape-matching algorithm in a receptor-based fashion, Ebalunode et al. developed a method that can be considered as a structure-based variant of ROCS. The method, SHAPE4... 

Hawkins, P. C., Skillman, A. G., Nicholls, A. (2007) Comparison of shape-matching and docking as virtual screening tools. /Med Chem 50, 74-82. 

J., Zheng, W. (2008) Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques. / Chem Inf Model 48, 889-901. 

We have done most of our studies on granular PTFE by compacting it into a preform and sintering to make a shape matching ASTM D-1708-66 for tensile testing. Orientation measurements by IR dichroism require thinner specimens, and for this purpose we used dispersion-grade material, commercially cast and processed into film (Dilectrix Corp., Farmingdale, NY). These films were used as received without further heat treatment. ... 

The S02 fluorescence pulse shape matched that of the laser indicating that the excited state lifetime was short compared to 1 ys. This implied that the short lived SO2 B2 (T< 35 ns) state was being excited by pumping hot bands of the SO2 1A1 ground state at 266.5 nm. 

Meyer et al.49 Complete enumeration (FFT) Hydrogen-bond filtering and shape matching 6 ca. 1.5 A lh... 

Ritchie and Kemp51 Complete enumeration (polynomial expansion) Electrostatic and shape matching 6 Depends on degree of polynomial used ih... 

Hendrix and Kuntz53 Geometric hashing/ site-point matching + EM Shape matching + MM 6 ca. 1 A ih... 

TOP) WHEN TWO PROTEINS BIND SPECIFICALLY, THEIR SHAPES MATCH EACH OTHER CLOSELY. (BOTTOM) TO CATALYZE A CHEMICAL REACTION AN ENZYME POSITIONS GROUPS CLOSE TO THE CHEMICAL THAT IT BINDS. THE SCISSORS REPRESENTS GROUPS ON THE PROTEIN THAT WILL CHEMICALLY CUT A SPECIFIC MOLECULE, REPRESENTED BY THE LIGHT-COLORED SHAPE. 

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