Molecular comparison

Williams, P. A. Phillips, G. O. Stephen, A. M. (1990). Spectroscopic and molecular comparisons of three fractions from Acacia Senegal gum. Food Hydrocolloids, Vol.4, No.4, (December 1990), pp. 305-311, ISSN 0268-005X. 

The pragmatic beauty of the chemical fingerprint is that the more common features of two molecules that there are, the more common bits are set. The mathematic approach used to translate the fingerprint comparison data into a measure of similarity tunes the molecular comparison [5]. The Tanimoto similarity index works well when a relatively sparse fingerprint is used and when the molecules to be compared are broadly comparable in size and complexity [5]. If the nature of the molecules or the comparison desired is not adequately met by the Tanimoto index, multiple other indices are available to the researcher. For example, the Daylight software offers the user over ten similarity metrics, and the Pipeline Pilot as distributed offers at least three. Some of these metrics (e.g., Tversky, Cosine) offer better behavior if the query molecule is significantly smaller than the molecule compared to it. 

Sansonetti PJ, d Hauteville H, Ecobichon C, Pourcel C Molecular comparison of virulence plasmids in Shigella and enteroinvasive... 

Gohlke, H. and Klebe, G. DrugScore meets comfa adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein./. Med. Chem. 2002, 45, 4153-4170. 

FIGURE 10.1 A molecular comparison of gases, liquids, and solids, (a) In gases, the particles feel little attraction for one another and are free to move about randomly, (b) In liquids, the particles are held close together by attractive forces but are free to move over one another, (c) In solids, the particles are rigidly held in an ordered arrangement. 

The fitness functions embodied in molecule-based methods are relatively fast, especially when optimisation is based on 2D properties, since they typically involve a pairwise molecular comparison with a target molecule rather than the analysis of an entire library, as is the case in library-based methods. However, there is no guarantee that building libraries from frequently occurring reactants will result in optimised libraries, nor is it possible to optimise properties of the library as a whole. 

Biocomputing, Big Island, Hawaii, January 4-9, 1999, pp. 482-493. Application of Parameter Optimization to Molecular Comparison. 

Back, K. and Chappell, J. (1995) Cloning and bacterial expression of a sesquiterpene cyclase from Hyoscyamus muticus and its molecular comparison to related terpene cyclases. /. Biol. Chem., 270, 7375-81. 

Method of Identiflcation and Molecular Comparison to the Noncovalent Dimer... 

Aprison, M.H., Galvez-Ruano, E. and Lipkowitz, K.B. (1995). On a Molecular Comparison of Strong and Weak Antagonists at the Glycinergic Receptor. J.Neur.Res., 41,259-269. 

Molecular Manipulation and Superimposition. To facilitate molecular comparisons, a variety of computer graphic techniques are available for three-dimensional manipulation and display of the stored structures in the library file (12,13). In our laboratory lateral stereo pair views of either single line or ball and stick models are displayed on a Tektronix 4014 graphics terminal linked to a Univac 1100/42 computer. 

Lemmen, C., et al., Application of parameter optimization to molecular comparison problems. Pac Symp Biocomput, 1999 p. 482-93. 

These molecular comparisons suggest that one binding site for oxidase or reductase is at the heme crevice on the face of the molecule, and the other one is also next to the heme crevice on the top. There is insufficient evidence at present to say which is which. Blocking residue 13 on the edge of the upper part of the creviee interferes with oxidase binding but not that of reductase, yet the positions that have been implicated in pyridoxal phosphate interference with reductase binding are in the same part of the molecule. It would be of great value to have selective modifications of lysines 79, 5, and 8, and 87-89, and to see the relative effects of each on oxidation and reduction. 

Kruger, N.J. Hammond, J.B.W. Molecular comparison of pyrophosphate-and ATP-dependent D-fructose 6-phosphate 1-phosphotransferase from potato tuber. Plant Physiol, 86, 645-648 (1988)... 

Various means and ways of molecular comparisons have been duly reeognized as stated under ... 

Besides, the molecular comparisons also embrace several critical and vital aspects to expatiate molecular modeling in drug design, such as volume mapping, locus maps, vector maps and conformational mimicry, directionality, and field effects. 

It is well known that the eDF can be used for computing molecular expectation values. However, from the point of view of the development of practical applications, first order DF beginning with ab initio functions and ending as well into Atomic Shell Approximation (ASA) forms [39], are accepted work candidates for QSM applications too [40]. General QSM definition proves to contain expectation values as a particular case [41], some summarised details can be found in Appendix A. First-order eDF are customarily used in QSM molecular comparisons, since the initial description of the original concept [16]. Higher order eDF can be employed as well in QSM calculations [31,33,35]. Problems consisting in systems other than molecules can be studied in the same way [41], and the QSM applications can be extended to the area of statistical mechanics distributions [43] as well. 

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