Canonical Numbering and Constitutional Symmetry

Ivanciuc, Ovidiu

doi:10.1002/9783527618279.ch7a

Cited by 10 publications

(45 citation statements)

References 52 publications

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“…The problem is that same molecule or part of such can be written as many different valid SMILES representations. Canonicalization [29] eliminates the problem for whole compound matches, but partial matches are widely considered troublesome. Small chemical changes sometimes alter the entire canonical representation.…”

Section: Smiles Regexmentioning

confidence: 99%

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Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

Robson

Dettinger³

et al. 2011

J Comput Aided Mol Des

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A patent data base of 6.7 million compounds generated by a very high performance computer (Blue Gene) requires new techniques for exploitation when extensive use of chemical similarity is involved. Such exploitation includes the taxonomic classification of chemical themes, and data mining to assess mutual information between themes and companies. Importantly, we also launch candidates that evolve by "natural selection" as failure of partial match against the patent data base and their ability to bind to the protein target appropriately, by simulation on Blue Gene. An unusual feature of our method is that algorithms and workflows rely on dynamic interaction between match-and-edit instructions, which in practice are regular expressions. Similarity testing by these uses SMILES strings and, less frequently, graph or connectivity representations. Examining how this performs in high throughput, we note that chemical similarity and novelty are human concepts that largely have meaning by utility in specific contexts. For some purposes, mutual information involving chemical themes might be a better concept.

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Section: Smiles Regexmentioning

confidence: 99%

“…Refs. [21][22][23][24][25][26][27][28][29][30][31]). We use regular expressions (''regex'') [19] in the Perl environment [20] in order to manage both SMILES and graph (connectivity) representation.…”

Section: Familiar and Novel Features Of This Workmentioning

confidence: 99%

Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

Robson

Dettinger³

et al. 2011

J Comput Aided Mol Des

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“…Also CIP designators only describe absolute and not relative stereochemistry. Stereo perception appropriate to synthetic analysis describes stereocenters in terms of ordered lists of substituents around each stereocenter or alternatively as local parity values related to the atom numbering used in the connection table 64…”

Section: Target and Precursor Perceptionmentioning

confidence: 99%

Computer‐aided synthesis design: 40 years on

Cook

Johnson

Law³

et al. 2011

WIREs Comput Mol Sci

101

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The discipline of retrosynthetic analysis is now just over 40 years old. From the earliest day, attempts were made to incorporate this approach into computer programs to test the extent in which chemical perception and synthetic thinking could be formalized. Despite pioneering research efforts, computer‐aided synthetic analysis failed to achieve widespread routine use by chemists, which can be attributed in part to the difficulty of building the required high‐quality retrosynthetic transform databases required for credible analyses. However, with the advent over the past 25 years of large comprehensive reaction databases, work on successfully automating the construction of reliable and comprehensive reaction rule databases is promising to revitalize research in this field. This review compares and contrasts the diverse approaches taken by selected programs in both the design and implementation of molecule feature perception and reaction rule representation, and we review the concepts of synthetic strategy selection, representation, and execution. In particular, we discuss the current work on automating the construction of reliable and comprehensive synthetic rule sets from available reaction databases in newer programs such as ARChem. We argue that the progress achieved in this aspect paves the way to a deeper exploration of computer approaches to applying strategy and control in the synthesis problem. © 2011 John Wiley & Sons, Ltd. This article is categorized under: Computer and Information Science > Chemoinformatics

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“…The constitutional symmetry is important for the interpretation of NMR and ESR spectra. Computer-assisted structure elucidation systems also use this information [1]. The correct determination of the symmetry classes for the atoms in a molecular graph is a basis for nding a canonical ordering of the atoms in a molecule, which in turn is necessary for generating a unique representation of the molecule [1].…”

Section: Introductionmentioning

confidence: 99%

“…Computer-assisted structure elucidation systems also use this information [1]. The correct determination of the symmetry classes for the atoms in a molecular graph is a basis for nding a canonical ordering of the atoms in a molecule, which in turn is necessary for generating a unique representation of the molecule [1]. This approach is used in the canonicalization algorithms for the linear representations of the molecular graphs like SMILES [2,3,4,5] and InChI [4,6].…”

Section: Introductionmentioning

confidence: 99%

Atomic Ring Invariant and Modified CANON Extended Connectivity Algorithm for Symmetry Perception in Molecular Graphs and Rigorous Canonicalization of SMILES

Krotko¹

2020

Preprint

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We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the highly symmetrical molecular graphs using traditional local and distance atom invariants. Also, we propose modifications of Weininger’s CANON algorithm to avoid its ambiguities (swapping and leveling ranks, incorrect determination of symmetry classes in non-aromatic annulenes, arbitrary selection of atom for breaking ties). The atomic ring invariant and the Modified CANON algorithm allow us to create a rigorous procedure for the generation of canonical SMILES which can be used for accurate and fast structural searching in large chemical databases.

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Canonical Numbering and Constitutional Symmetry

Cited by 10 publications

References 52 publications

Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

Computer‐aided synthesis design: 40 years on

Atomic Ring Invariant and Modified CANON Extended Connectivity Algorithm for Symmetry Perception in Molecular Graphs and Rigorous Canonicalization of SMILES

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