Chemical encoding

A year later, a novel method of encoding chemical structures via typewriter input (punched paper tape) was described by Feldmann [42]. The constructed typewriter had a special character set and recorded on the paper tape the character struck and the position (coordinates) of the character on the page. These input data made it possible to produce tabular representations of the structure. 

At the low end of the hierarchy are the TS descriptors. This is the simplest of the four classes molecular structure is viewed only in terms of atom connectivity, not as a chemical entity, and thus no chemical information is encoded. Examples include path length descriptors [13], path or cluster connectivity indices [13,14], and number of circuits. The TC descriptors are more complex in that they encode chemical information, such as atom and bond type, in addition to encoding information about how the atoms are connected within the molecule. Examples of TC descriptors include neighborhood complexity indices [23], valence path connectivity indices [13], and electrotopological state indices [17]. The TS and TC are two-dimensional descriptors which are collectively referred to as TIs (Section 31.2.1). They are straightforward in their derivation, uncomplicated by conformational assumptions, and can be calculated very quickly and inexpensively. The 3-D descriptors encode 3-D aspects of molecular structure. At the upper end of the hierarchy are the QC descriptors, which encode electronic aspects of chemical structure. As was mentioned previously, QC descriptors may be obtained using either semiempirical or ab initio calculation methods. The latter can be prohibitive in terms of the time required for calculation, especially for large molecules. 

Christensen T. A., Heinbockel T. and Hildebrand J. G. (1996) Olfactory information processing in the brain encoding chemical and temporal features of odors. J. Neurobiol. 30, 82-91. 

NORDLUND, D.A., Semiochemicals A review of the terminology, in Semiochemicals. Their Role in Pest Control (D.A. Nordlund, R.L. Jones and W.J. Lewis, eds.), John Wiley Sons, New York. 1981, pp. 13-28. CHRISTENSEN, T.A., HEINBOCKEL, T., HILDEBRAND, J.G., Olfactory information processing in the brain encoding chemical and temporal features of odors, J. Neurobiol., 1996, 30, 82-91. 

Oligonucleotide-encoded chemical synthesis proposed by Lerner and Brenner (Proc. Natl. Acad. Sci. USA, 1992, 89, 5181)... 

Only a few compounds screened in early lead identification phases are synthesized in-house. More flexible and cost effective is to purchase chemicals from external suppliers. Most vendors provide lists of some ten to himdred thousand chemicals on compact discs and guarantee delivery within days to weeks. To explore this huge amount of data with the aid of computers, chemical information is transformed to computer-readable strings, e.g., smiles code, and different descriptors are determined. 1-dimensional (1-D) descriptors encode chemical composition and physicochemical properties, e.g., molecular weight, stoichiometry (C O Hj,), hydrophobicity, etc. 2-D descriptors reflect chemical topology, e.g., connectivity indices, degree of branching, number of aromatic bonds, etc. 3-D descriptors consider 3-D shape, volume or surface area. 

The advantage of matrix representation consists of the fact that all of the matrix operations can be applied to the encoded chemical structures. Simple subtraction of two BE matrices provides. 

First, a large polysaccharide, with extensive repetitive sequences and local regions that are irregular or branched, may be a structure in which encoded chemical signals, in a form such as oligosaccharide sequences, are maintained in a fixed spatial array. 

N. Krall, J. Scheuermann, and D. Neri, Small Targeted Cytotoxics Current State and Promises from DNA -Encoded Chemical Libraries. Angew. Chem. Int. Ed., 52 (2013) 1384-1402. 

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