Assemble 2.0: a structure generator

Badertscher, Martin; Korytko, Andrew I.; Madison, Mark S.; Munk, Morton E.; Portmann, Pius; Junghans, Martin; Fontana, Patrick; Pretsch, Ernö

doi:10.1016/s0169-7439(00)00056-3

Cited by 31 publications

(27 citation statements)

References 17 publications

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“…SESAMI (systematic elucidation of structure applying machine intelligence) includes a 2D NMR interpretation module, INTERPRET2D, which can be linked to the structure generators ASSEMBLE, 11 COCOA, 12 and the latest generator HOUDINI. 13 The general workflow of the system does not markedly depend on the type of structure generator used.…”

Section: Sesami-cmentioning

confidence: 99%

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CASE 2D NMR-based Expert Systems

2011

Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation

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Modern expert systems utilize 1D and 2D NMR data. The 2D NMR expert systems described in the literature over the last two decades will be reviewed as these form the foundation of understanding from which modern systems have been developed. These systems include the SESAMI, CISOC-SES, LSD, COCON and LUCY systems. These systems have previously demonstrated the possibility of elucidating structures common to organic chemistry utilizing 1H-1H COSY-connectivities, one-bond and long-range 1H-13C correlations. These systems have paved the way for the development of the most effective strategies for the application of expert systems.

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Section: Sesami-cmentioning

confidence: 99%

“…In this example, the MAX-ERR-LRDC value was set to zero. This did not hinder the identification of a correct result, since the two non-standard COSY correlations (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21) and (4-9), indicated by arrows in the structure 6.1, had been extended to 3-5 bonds.…”

Section: The Expert System Cisoc-sesmentioning

confidence: 99%

CASE 2D NMR-based Expert Systems

2011

Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation

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“…Originalmente um puro gerador de estruturas, recentemente propagandeado como um módulo independente, está na versão 2.0 55 . Não realiza interpretação de espectros, baseando-se puramente nas informações fornecidas pelo usuário, que deve realizar a sua interpretação.…”

Section: Assembleunclassified

Elucidação estrutural de substâncias orgânicas com auxílio de computador: evoluções recentes

Stefani¹,

Nascimento²,

Costa³

2007

Quím. Nova

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“…CONGEN was the structure generator developed within DENDRAL, which preceded a more advanced generator known as GENOA [3]. Many commercial structure generators were developed later, most renowned ones being CHEMICS [4], ASSEMBLE [5], SMOG [6], and the most widely used of all of them, the general purpose structure generator MOLGEN [7]. These closed source software tools work like a black box, where the user cannot, on the one hand, understand the functioning of the software and on the other hand, customize the tool to his needs.…”

Section: Introductionmentioning

confidence: 99%

OMG: Open Molecule Generator

et al. 2012

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Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

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Assemble 2.0: a structure generator

Cited by 31 publications

References 17 publications

CASE 2D NMR-based Expert Systems

CASE 2D NMR-based Expert Systems

Elucidação estrutural de substâncias orgânicas com auxílio de computador: evoluções recentes

OMG: Open Molecule Generator

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