Domains definition from structure

Inspection of protein structures can show which regions of a protein form compact globular structure and hence the domains of the protein. Several methods can be used to automatically extract domain definitions from three-dimensional structures (Holm and Sander, 1995 Islam et al.,... 

Sowdhamini et al., 1996 Taylor, 1999). These methods agree on the domain boundary definitions for the majority of known structures, but each method predicts some domains differendy from those defined by biologists (Jones et al., 1998). The definition of domains suggests that they should be discrete and therefore able to be expressed in isolation. This has been demonstrated for many domains however, in some cases, clearly accepted domains are not stable in isolation. 

One of the most important problems in QSAR analysis is establishing the domain of applicability for each model. In the absence of the applicability domain restriction, each model can formally predict the activity of any compound, even with a completely different structure from those included in the training set. Thus, the absence of the model applicability domain as a mandatory component of any QSAR model would lead to the unjustified extrapolation of the model in the chemistry space and, as a result, a high likelihood of inaccurate predictions. In our research we have always paid particular attention to this issue (12, 20-27). A good overview of commonly used applicability domain definitions can be found in reference (28). 

A further feature of the structure of the functional domain arises from the central role of the irreducible element in the description of functionality and the definition of that element, as depicted in Fig. C4.4. Due to this view of an engineering project as an optimisation of the balance between cost and revenue, the secondary elements fall into two completely separate categories the elements describing aspects of the cost, and the elements describing aspects of the performance, as already mentioned at the end of Sec. C4.3 and illustrated in Fig. C4.6. 

The aldehyde oxidoreductase from Desulfovibrio gigas shows 52% sequence identity with xanthine oxidase (199, 212) and is, so far, the single representative of the xanthine oxidase family. The 3D structure of MOP was analyzed at 1.8 A resolution in several states oxidized, reduced, desulfo and sulfo forms, and alcohol-bound (200), which has allowed more precise definition of the metal coordination site and contributed to the understanding of its role in catalysis. The overall structure, composed of a single polypeptide of 907 amino acid residues, is organized into four domains two N-terminus smaller domains, which bind the two types of [2Fe-2S] centers and two much larger domains, which harbor the molybdopterin cofactor, deeply buried in the molecule (Fig. 10). The pterin cofactor is present as a cytosine dinucleotide (MCD) and is 15 A away from the molecular surface,... 

Signals used in analytical chemistry have a definite origin from particular species or given structural relationships between constituents of samples. The relation of the sample domain and the signals domain, i.e. the coding and decoding process as represented in Fig. 2.12, must be as unambiguous as possible. 

Synopsis of Experiment and Results. The material is irradiated during straining and relaxation. The example shows that a nanostructure which is hard to interpret from a series of scattering patterns may clearly reveal its complex domain structure after transformation to the CDF. Different structural entities are identified which respond each in a different way on mechanical load. The shape of the basic particles is identified (cylinders). The arrangement of the cylinders is determined. Thus the semi-quantitative analysis of the CDF provides the information necessary for the selection and definition of a suitable complex model which is required for a... 

The examples cited in this chapter are but a rather small and arbitrary selection from the richly varied possibilities for supramolecular bonding. Recognition of the intrinsic chemical (partially covalent, exchange-type) character of supramolecular interactions leads inevitably to an extended definition of chemistry that includes many aspects of nanoscale aggregation, structure, and function in the biophysical and material-science domains. From this viewpoint, the molecule is seen to be... 

Although definitive structural solutions for any of the prion domain filaments have yet to be achieved, the body of experimental data is growing and it is possible that the fold and packing of prion domains in HET-s filaments differ qualitatively from those in Ure2p or Sup35p filaments (Section VI). 

Domains may be regarded as the basic units for the structure, function and evolution of proteins, but the definition of a domain remains fuzzy. They are most often treated as compact or connected areas that are apparent from a visual inspection of protein models. To avoid subjectivity and ambiguities of visual inspection, computer algorithms have been developed to localize domains. Rashin offered an alternative interpretation domains are stable globular fragments, generated in biochemical experiments that refold autonomously and retain specific functions. He proposed a method for localiz-... 

Pores may be present as structural features (e. g. between domains) or as a result of aggregation of particles. They may also be the result of partial dehydroxylation (oxide hydroxides) or dissolution. Although the shapes of pores can be quite variable, there are some definite, basic forms. The commonest of these are 1) slit shaped, the walls of which may or may not be parallel 2) ink bottle which are closed upon all sides but one from which a narrow neck opens and 3) cylindrical. Upon partial dissolution, pores bounded by well-defined crystal planes (e. g. 102 in goethite) develop (Chap. 12). 

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