Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs

Faulon, Jean‐Loup

doi:10.1021/ci9702914

Cited by 61 publications

(74 citation statements)

References 29 publications

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“…For chemical subgraph searches this time-consuming step at best runs in polynomial time. 16 To speed up the process we apply a two-step procedure of a fingerprint based prescreening followed by a full subgraph matching in the screening result. Fingerprints are one-dimensional bit arrays, where bits are set according to the occurrence of a particular structural feature.…”

Section: User-defined Database Functions Specific To Chemistrymentioning

confidence: 99%

NMRShiftDBConstructing a Free Chemical Information System with Open-Source Components

Steinbeck

Krause

Kühn

2003

J. Chem. Inf. Comput. Sci.

142

140

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The process of designing and implementing NMRShiftDB, an open-source, open-content database for chemical structures and their NMR data based solely on free software is described. NMRShiftDB is available to the community on http://www.nmrshiftdb.org. It allows for open submission and retrieval of data sets by its user community. The software and the content itself is freely distributable, allowing for the establishment of a highly available mirror system of databases in collaborating laboratories.

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Section: User-defined Database Functions Specific To Chemistrymentioning

confidence: 99%

NMRShiftDBConstructing a Free Chemical Information System with Open-Source Components

Steinbeck

Krause

Kühn

2003

J. Chem. Inf. Comput. Sci.

142

140

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“…The first is the Moscow school around Academician Nikolai Serafimovich Zefirov, that includes Drs Palyulin, Skvortsova, and Baskin [49][50][51][52][53][54][55][56][57][58][59][60]. Another remarkable group is around Dr Jean-Loup Faulon [61][62][63][64][65][66][67][68]. Professors Lemont B. Kier and Lowell H. Hall have published several papers on this topic [69][70][71].…”

Section: Triplet and Kier-hall Indices With Very Low Degeneracy Corrementioning

confidence: 99%

Can topological indices transmit information on properties but not on structures?

Balaban

2005

J Comput Aided Mol Des

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A survey of several topological indices (TIs) is provided according to the nature (integers or real numbers) of the local vertex invariants (LOVIs) and of the resulting molecular descriptor (TI). The 1st generation TIs such as the Wiener index when both the LOVIs and the TI are integers have a very high degeneracy. This fact can become an asset for the problem under discussion: when confronted with the "inverse problem" (reverse engineering) such indices lead to a combinatorial explosion of possible solutions. On the other extreme, TIs with very low degeneracy may also offer the possibility to transmit information on properties but not on structures, because they may be too difficult to lend themselves to reverse engineering in a reasonable amount of time. Several such indices are discussed: the novel second-generation index G (derived from the average distance-based connectivity index J in order to include a dependence on graph size and cyclicity), and third-generation indices such as the triplet TI denoted by DN2S(4) or the Kier-Hall index TOTOP. The intercorrelation of these indices is discussed: G is almost linearly-correlated with DN2S(4), and shows a different type of correlation with TOTOP.

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“…In the graphical method of representation, the reaction rules take the form of graph rewriting rules, with subgraphs replacing the regular expressions of BioNetGen. This new approach to model specification is inspired by the use of graphs and graph rewriting rules to model chemical systems (for examples, see [21,22,[71][72][73][74]). The literature about the use of rules, including graph rewriting rules, to model systems is substantial.…”

Section: Discussionmentioning

confidence: 99%

Rule‐based modeling of biochemical networks

Faeder¹,

Blinov²,

Goldstein³

et al. 2005

Complexity

120

136

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We present a method for generating a biochemical reaction network from a description of the interactions of components of biomolecules. The interactions are specified in the form of reaction rules, each of which defines a class of reaction associated with a type of interaction. Reactants within a class have shared properties, which are specified in the rule defining the class. A rule also provides a rate law, which governs each reaction in a class, and a template for transforming reactants into products. A set of reaction rules can be applied to a seed set of

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Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs

Cited by 61 publications

References 29 publications

NMRShiftDBConstructing a Free Chemical Information System with Open-Source Components

NMRShiftDBConstructing a Free Chemical Information System with Open-Source Components

Can topological indices transmit information on properties but not on structures?

Rule‐based modeling of biochemical networks

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