Restriction site distance methods

Although distance methods have certain advantages for the analysis of restriction site data, notably their computational efficiency, they also have an important disadvantage. By reducing the data to pairwise distances, important information on the evolutionary history of individual restriction sites is lost. In chloroplast DNA, for example, individual sites often evolve at very different rates. A parsimony analysis of 328 restriction site mutations shared among two or more taxa in a survey of 57 taxa from the sunflower family showed that 186 of the sites had only a single mutation, whereas 6 sites showed nine or more mutations.24 A conservative statistical... 

The location of the binding site can yield distance constraints to filter possible solutions and this is implemented in our procedure. An intermolecu-lar residue-residue interaction is defined if any pair of atoms is closer than a 4.5 A cut off. This cut off considers the probable error in conformation of any predicted complex. One feature of the Fourier correlation method implemented in FTDOCK, is that biological constraints on one molecule cannot be used to reduced the initial search. For any orientation of the movable molecule, it is placed at every translational position with respect to the static molecule. However, if constraints were available for both molecules, the range of orientations sampled by the movable molecule could be restricted. 

Cluster model scheme and periodical method were used in the molecular model calculations of active sites of zeolite catalysts results of both approaches are presented and discussed in this review. In cluster models of zeolite structures hydrogen boundary atoms (H ) were used to saturate dangling bonds of the Si and Al atoms. Definite restrictions were imposed on the optimization of positions of these boundary H atoms. In the optimization, the geometry of an appropriate fragment of zeolite lattice was taken from the experimental X-ray diffraction data [7]. Only Si-H and Al-H bond distances were optimized, while the positions of other atoms (except M), as well as directions of 0-H bonds, were kept frozen. The M ion was allowed to move freely in the structure. 

We must keep in mind that real surfaces are part of a usually disordered solid and in addition act as an inseparable ensemble of sites. Therefore, the analytical approach is restricted to methods that do not require free mobility of the target group or a long distance order of the solid. So the most powerful tools of the modem analytical chemistry, NMR (except MASNMR), and X-ray structure analysis, are ruled out. Others may be used with considerable limitations only. 

Figure 3 Structural alignments with discrete properties. Methods are based on discrete properties using the DG algorithm (1) or clique-detection (11) as implemented in distance comparisons (DISCO), and Apex-3D. The structure representation, based on discrete properties, resorts to one atomic descriptor (I), usually the atom type, or multiple atomic or site descriptors (II). In the first method (I), the conformational analysis is restricted to the generation of molecular geometries which allow a common arrangement of selected phaimacophoric moieties present in a rigid compound used as template. In the second method (II), the conformational analysis procedure may involve a systematic enumeration of all the possible conformadons for each ligand. The search similarity is directed towards the confirmation of a predefined pharmacophore postulated by the modeler or from some classical SAR in the case of the active analog approach (1), or the automated identification of pharmacophores and bioacdve conformations (II)...

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