String fragmentation

Figure 8.3 Example of a 2D similarity search, showing a query molecule and five of its nearest neighbors. The similarity measure for the search is based on 2D fragment bit-strings and the Tanimoto coefficient.

Although such a fragment-based measure clearly provides a very simple picture of the similarity relationships between pairs of structures, it is both efficient (because it involves just the application of logical operations to pairs of bit-strings) and effective (in that it is able to bring together molecules that are judged by chemists to be structurally similar to each other) in operation. 

MATERIALS Metal fragments (nails, washers, bolts, nuts, etc.), rags, wire, tape, or string, container, primacord and/or blasting caps, plastic explosive or dynamite. 

MATERIALS String, wire or tape, fragmentation grenades, primacord, blasting cap. 

In our example spectrum (Fig. 6.11), the majority of most intense peaks belong to N-terminal fragments, leaving only low intensity peaks for potential C-terminal ions. In such cases, care should be taken on peak annotation as such low intensity peaks can also result from detector noise. However, they can be used for sequencing as long we can see at least a two to three AA sequence string, and the information obtained this way is consistent with other results. 

A search for the singly charged N-terminal fragments shows that a peak at 922.5 corresponds to a loss of serine and alanine from the C-terminus. A shift of 128 Da specific for glutamine/lysine is also present (peak at 794.4 Th), but unfortunately, this sequence string cannot be extended any further. All that can be done is to find... 

The second approach is more time consuming but can provide more reliable results. As the sequence string covers most of the peptide s sequence, the unknown terminal fragments are no longer than two to three amino acids, so their masses may be specific enough to identify them. 

First of all, the shortest fragments in both b- and y-ion series should be available. Such ions can be used to assign the sequence strings to either N- or C-terminal ion... 

As already noted above, AFM imaging and quantitations on LH-stripped chromatin fibers revealed extended beads-on-a-string structures, in agreement with early EM results [17]. Nucleosomal arrays reconstituted from naked DNA fragments and histone octamers had similar appearance [36 2]. 

Holliday, J. D., Hu, C.-Y., and Willett, P. (2002) Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings. Combi. Chem. High Through. Screen. 5, 155-166. 

A] to form [(Tab)2M][Au(CN)2] units. Two such fragments are further connected by one gold-gold aurophilic bonding interaction [Au-Au 3.0140(5) A] to form an uncommon Ag-Au-Au-Ag linear string structure with three ligand-unsupported metal-metal bonds [605]. 

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