Structural error

Figure 17.2 An example of prediction of the conformations of three CDR regions of a monoclonal antibody (top row) compared with the unrefined x-ray structure (bottom row). LI and L2 are CDR regions of the light chain, and HI is from the heavy chain. The amino acid sequences of the loop regions were modeled by comparison with the sequences of loop regions selected from a database of known antibody structures. The three-dimensional structure of two of the loop regions, LI and L2, were in good agreement with the preliminary x-ray structure, whereas HI was not. However, during later refinement of the x-ray structure errors were found in the conformations of HI, and in the refined x-ray structure this loop was found to agree with the predicted conformations. In fact, all six loop conformations were correctly predicted in this case. (From C. Chothia et al.. Science 233 755-758, 1986.)...

Example 4. Stereochemical ambiguities and structural errors can be encountered in the Merck Index [20] as well, as shown in these two examples ... 

Ensure the validity of a structure by using structural information without obvious errors in the structural description. Some structural errors are identified by chance, and others appear in the process of 2D to 3D structure conversion, geometry optimisation, and descriptor calculation. We pay specific attention... 

Identification of the 1,2,4-triazole ring and location of its substituents can be decided on the evidence of synthesis and molecular formula in a few cases. However, the early literature abounds in structural errors resulting from unjustified confidence in elementary methods and from the absence of instrumental analysis that provides a variety of independent structural proofs in our days. A few examples Illustrate points to be kept in mind by sceptical triazole chemists. 

Notice the model structure is usually in error also, e.g., the true relationship between y and x may be nonlinear, variables other than x may be required to predict y, and so on. The procedure outlined here lumps structural error into e as well, but structural error is not accounted for correctly in this way. If the structure is in serious doubt, one may pose instead model discrimination tests to choose between competing models with different stnictures [30, 31 j. 

High-yield self-assembled DNA tile-templated AuNP nanoarrays with lesser error can be synthesized using an AuNP-DNA conjugation strategy. In complex structures error reduction can lead to a number of useful applications of self-assembled structures. Reduction of error starts before the actual assembly begins. The yield of... 

Figure 2.39 Comparison of the observed (5exp) and calculated ( cak) chemical shifts of Ala4 for (A) H, (B) and (C) (X-ray calculated based on single crystal X-ray structure and Opt geometry optimized structure). Error bars of the observed chemical shifts for H are FWHM determined from decomposition of 1D spectra. The error bars are added oniy Opt plots. The error bars of and are not shown because the FWHMs of all signals are smaller than plotted circles, which areO.2-0.8 ppm. Calculated chemical shifts are set to minimize RMSD between the calculated and the observed data. For NH3, the three calculated chemical shifts are averaged. Reprinted from Ref. [187] Copyright 2014 Wiley Periodical, Inc.

The design of the information resident in the SSR must be appropriate for its self-replication. Its characteristics must be complete and adequate for the task. It must cover all relevant aspects that intervene during replication (e.g., materials, parts, processes, procedures, plans, spatial structures, error and recovery handling, etc.). Completeness means also that the information designed and stored in the SSR is correctly correlated with the SSR environment. That means, for example, that the SSR design should be based on an accurate and exhaustive list of raw materials and raw parts that exist in the SSR environment together with the material identification... 

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