Molecular code similarity

Implementation of the whole set of integral algorithms within the ARIADNE molecular program [66a] as well as MOLSIMIL molecular Quantum Similarity code [66b], developed in our Laboratory is under way. A discussion on the sequential, vector and parallel programming features of the CETO integral calculation will be ptablished elsewhere. Perhaps other available ETO functions, left unexplored on this paper, will be studied in the near future and the... 

The strategy of this approach was to develop a set of molecular codes corresponding to the number of self-avoiding paths of each length in a molecule, for use both as a convenient representation in subsequent similarity searches [52-54], and as a quantitative measure of structural complexity. Since the basic calculation method for these codes was again based on counting bonds, it is easy to visualize how these path codes are related to the Weiner index (Fig. 13.1-3). While these initial molecular codes did not address... 

The development of DFT band structure calculations in the condensed matter physics community have followed a similar course as that described for the molecular codes in chemistry. DPT was... 

We will try to answer some of these questions in this chapter. The emphasis will be on representation and characterization of molecules rather than the questions concerning molecular similarity and structure-property relationships. We will differentiate between the representation and the characterization. The former is based on molecular codes and the latter on structural invariants. The codes allow one to represent a structure without loss of information, hence they allow one to reconstmct the object fully from a given code. Invariants represent mathematical properties of a structure and are therefore useful in structure-property analysis, as well as in comparisons of different stmctures. The list of invariants need not be unique, hence, invariants do not generally allow reconstruction. Figuratively speaking, characterization depicts various... 

In a series of articles Mezey and Arteca studied topological properties of molecular surfaces in order to quantify molecular shape. " They characterized the shape by considering curvatures of portions of the molecular surface that have distinct topological properties. We will focus attention on a characterization of the molecular shape by binary molecular codes. Instead of considering the general problem of molecular shapes, we will consider a simpler task, namely, the characterization of the shapes of planar benzenoids. It will be revealed that the approach applies to the characterization of the shape of an arbitrary closed planar curve. A satisfactory code for the periphery of a simple benzenoid should be linear, have structural origin, be simple, have similar lengths for objects of similar size, be unique, and should allow reconstruction. 

The recent highlighting of transport phenomena has focused research attention on its molecular aspects. The availability of high-level dynamic molecular codes has made possible the simulation of biological fluids similar to the actual conditions. Application to biological systems requires the inclusion of transport mechanisms that take into account the particular nature of cellular membranes and the phenomena of biological environments. 

The similarity matrices are constructed by one in-house program developed inside CHIRBASE using the application development kit of ISIS. They contain the similarity coefficients as expressed by the Tanimoto method. In ISIS, the Tanimoto coefficients are calculated from a set of binary descriptors or molecular keys coding the structural fragments of the molecules. 

Finally, also isolated from D. vulgaris was another homodimeric protein (subunit molecular mass of 27 kDa) named nigerythrin (43). Spectroscopic characterization revealed that this protein is similar to Rr. The function of nigerythrin is also unknown. It should be noted that genes coding for two similar Rr proteins were also found in Arch-aeoglobus fulgidus. 

It has been postulated that Chlamydia may produce a heat shock protein that causes tissue damage through a delayed hypersensitivity reaction. C. trachomatis may also possess DNA evidence of toxin-like genes that code for high-molecular-weight proteins with structures similar to Clostridium difficile cytotoxins, enabling inhibition of immune activation. This may explain the observation of a chronic C. trachomatis infection in subclinical PID. 

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