Toward a global maximization of the molecular similarity function: Superposition of two molecules

Constans, Pere; Amat, Lluı́s; Carbó‐Dorca, Ramon

doi:10.1002/(sici)1096-987x(19970430)18:6<826::aid-jcc8>3.0.co;2-u

Cited by 101 publications

(92 citation statements)

References 40 publications

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“…or aligning the molecules so that the resulting molecular similarity is maximized (QSSA 43,44,45,46,47 ). It deserves mentioning that for a true distance, one can demand internal consistency over a molecular set 46 .…”

Section: Alignment Of the Enantiomersmentioning

confidence: 99%

Alternative Kullback−Leibler Information Entropy for Enantiomers

et al. 2009

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Section: Alignment Of the Enantiomersmentioning

confidence: 99%

Alternative Kullback−Leibler Information Entropy for Enantiomers

et al. 2009

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“…Molecular similarity analysis has a very extensive literature, initiated by the early works of Carbo and others [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20], and depending on the focus of the similarity study, the quantum similarity approach, or the Shape Group approach [21][22][23][24], or some simpler, specialized approaches [24,25] may be the optimum choice.…”

Section: Introductionmentioning

confidence: 99%

Fragment shape variation index for periodicity deficiency and gradual changes of internal coordinates along linear polymers

Simon

Mezey

2011

J Math Chem

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A special adaptation of the fragment shape variation index approach is applied to a series of rod-like structures obtained by replacing all C-C atom pairs by B-N atom pairs in linear polymers constructed by stacking adamantane units on top of each other. A special feature of these structures is a systematic, monotonic increase of the length of B-N bonds roughly parallel with the axis of the rods when moving from the B-terminus towards the N-terminus of the rods. All other changes in the unit cells of these short polymers are less important and less systematic, consequently, focusing on these B-N bonds of the given structures is especially suitable for the application of the fragment shape variation index approach used for a single type of internal coordinate shape descriptor. The results reveal additional trends which are easy to miss if one is restricted to a simple inspection of the data. The study also confirms that in special cases one may replace the detailed electron density shape descriptors with the far simpler bond length data as formal, but limited shape descriptors, whenever the overall structures and shapes show only minor changes, affecting primarily only one type of the internal coordinates.

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“…The quantum similarity measurements (QSM) are based on a quantitative comparison of electronic densities of two molecules superposed and aligned to optimize a well-defined similarity function [5][6][7][8][9]. This procedure leads to nuclear distances smaller than usually encounter in molecular bonds.…”

Section: Introductionmentioning

confidence: 99%