Fragment SMARTS

This function computes the polar surface area of an input SMILES structure. It uses the table for tpsa fragment SMARTS and fragment partial polar surface areas shown in Table A.3. It relies on the count matches function described in Chapter 7. 

A variety of domain or motif families occur only as extensions to other domains. The Bruton s tyrosine kinase motif (BTK), for example, is found only at the C terminus of PH domains. Similarly, a C-terminal extension (the S TK X domain) to some subfamilies of serine/threonine kinases (S TK) is not found in isolation. Cases where only the extension, and not the preceding domain, is found are strong evidence that the proteins are wrongly assembled from genomic sequence or else represent partial cDNA sequences (Fig. 9, see Color insert). Indeed, all five proteins annotated in SMART as containing a S TK X domain with no catalytic domain are noted to be fragments in their corresponding sequence database entries. 

Smart hydrogels have found use in bioseparation. Materials responsive to temperature were used in liquid chromatography and electrophoretic applications, to separate proteins, steroids and DNA fragments. Antibody-containing materials for the concentration of antigens were also described. 

A descriptor center finally consists of a structural part (e.g., atom, multiple similar atoms, pseudoatoms, fragments) and a property. To define this structural part efficiently, the line notation SLang is used, which is similar to simplified molecular input line enky specification (SMILES) and SMILES arbitrary target specification (SMARTS) [12]. Examples for structural parts and their representations in SLang are as follows ... 

Create Table fragments (description Text, smarts Text, abit Integer) ... 

The column named smarts contains the SMiles ARbitrary Target Specification (SMARTS) pattern defining the fragment. The column named... 

Table 8.1 Simple Fragment Keys Defined Using SMARTS...

Select abit from fragments Where matches ( clccccclO, smarts) ... 

The simplest molecular property is molecular weight. The obvious fragments to use for this are atoms. It is a simple matter to define the SMARTS fragments for any atom. Table 8.2 shows the definition for a few common atoms. The full table for the first 103 atoms is shown in the Appendix. 

The following function is analogous to the fragment key function above. It uses a relational table to define fragments, a function to match SMILES and SMARTS (in this case count matches), and an aggregate SQL function to tally the results over all matched fragments. 

Another useful fragment-based function computes the polar surface area of a molecule using the method described by Ertl, Rohde, and Selzer.7 The SMARTS and partial surface areas for the fragments described by Ertl are shown in Table A.3 in the Appendix. That table is created as... 

Table A.3 shows SMARTS for fragments described by Ertl, Rhode, and Selzer.2 It contains the SMARTS definition of the fragment and the fragment partial polar surface area. This table is used in the tpsa function to compute the polar surface area for a molecular structure.

Table A.4 shows commonly used fragment keys the MACCS publicl66-keys. This table is used with the publicl66keys function above to produce a bit string key for use in filtering before substructure searching and for similarity computations. The table consists of SMARTS patterns3 used to identify each of 166 substructures.

FIGURE 10.3 Schematic view of the stimuli-responsive association of smart polymer chain fragments in aqueous solution. 

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