Computer assisted structure elucidation of natural products using two-dimensional NMR spectroscopy†

Jaspars, Marcel

doi:10.1039/a804433c

Cited by 59 publications

(61 citation statements)

References 29 publications

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“…Much effort has thus been devoted to dwindling the search space before the real generation and evaluation step, by deducing more structural constraints from the spectra data with the help of previous knowledge accumulations. 1,[5][6][7] Libraries of structural fragments connected to certain spectral features are a typical way to dramatically decrease the size of the search space by combining nodes from the atom set into larger fragments, with those atoms thus no longer taking part in the combinatorial process. In the case of proton-rich compounds, large numbers of constraints derived from 2D NMR long-range correlations also cut down the search space significantly.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation

Han

Steinbeck

2004

J. Chem. Inf. Comput. Sci.

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An evolutionary algorithm (EA) using a graph-based data structure to explore the molecular constitution space is presented. The EA implementation proves to be a promising alternative to deterministic approaches to the problem of computer-assisted structure elucidation (CASE). While not relying on any external database, the EA-guided CASE program SENECA is able to find correct solutions within calculation times comparable to that of other CASE expert systems. The implementation presented here significantly expands the size limit of constitutional optimization problems treatable with evolutionary algorithms by introducing novel efficient graph-based genetic operators. The new EA-based search strategy is discussed including the underlying data structures, component design, parameter optimization, and evolution process control. Typical structure elucidation examples are given to demonstrate the algorithm's performance.

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Section: Introductionmentioning

confidence: 99%

Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation

Han

Steinbeck

2004

J. Chem. Inf. Comput. Sci.

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“…22 -24 At the beginning of the search of the structure of an a priori unknown substance, the first question that should arise is 'Has this substance been already isolated and characterized?' This means that dereplication should precede elucidation.…”

Section: Structure Elucidationmentioning

confidence: 99%

Automated Interpretation of NMR Spectra for Small Organic Molecules in Solution

Nuzillard

2014

eMagRes

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The interpretation of NMR spectra of small organic molecules is first considered as the method of extracting the chemical shifts and coupling constant spectral parameters from 1 H NMR spectra and then as the means of establishing relationships between spectra and the structure of small organic molecules. Spectral interpretation is discussed in the latter understanding for applications in structure verification and structure elucidation.

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“…[9] Furthermore, a team of experienced researchers is also needed, as interpretation through raw data from those chemical instruments has been a "bottleneck" step at BioDiscovery research. [10][11][12] All of these factors have become the main problems for institutions or universities in Indonesia, as a developing country, to start BioDiscovery exploration on its own marine organisms. Therefore, international collaborations with developed countries researchers have been conducted by many Indonesian institutions.…”

Section: Introductionmentioning

confidence: 99%

North-South BioDiscovery Research Collaboration of Indonesian Sponge and Soft Coral : A Bibliographic Analysis of Publications Over the Last Two Decades

Januar¹

2016

J. Scientomet Res.

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Context:The tropical Indonesian sponges and soft corals species are valuable resources that produce bioactive chemical compounds. However, BioDiscovery on those compounds requires adequate budget, modern laboratory, and skilful researchers. To foster capacity building, international collaborations with developed countries researchers have been conducted by various Indonesian institutions. In return, developed countries researchers were granted access to the tropical biodiversity resources. Aims: This study presents evaluation of Indonesian capacity development during international collaborative research on BioDiscovery of natural products from Indonesian sponges and soft corals over the last two decades. Methods and Material: Valuation had been done by bibliometric analysis, based on the authorship of Indonesian researchers in publications at major international journals on the theme of natural products BioDiscovery. Results: The study showed there were 104 publications between the year of 1994 to 2015 that reported 328 new compounds from Indonesian sponges and soft corals. Among those works, Indonesian researchers contributed as an author in 49% publications. However, the role as a principal researcher (1 st author) was low (14%). Furthermore, unequal benefit sharing of research results showed, as roughly 40% of those publications did not include or acknowledge any Indonesian collaborators. All of these reflect unequal benefit sharing, and capacity of Indonesian researchers on this particular field has not been successfully developed as expected. Conclusion:The paradigm of "biodiversity data trade" and "parachute science" needs to be changed. However, it requires government support in biogenetic conservation and material transfer traceability towards equitable benefit sharing of BioDiscovery research results.Key words: Authorship, BioDiscovery, Indonesia, Soft coral, Sponge. Key MessagesThe practices of unequal academic benefit sharing and capacity building on international BioDiscovery need to be avoided and this requires government support from both collaborators to encourage biogenetic conservation and material transfer traceability implementation, towards equitable benefits sharing of BioDiscovery research results. International North-South collaboration on marine BioDiscovery research, as it shows between developed countries and Indonesia over the last two decades, requires government support from both collaborators to encourage biogenetic conservation and material transfer traceability implementation, towards equitable benefits sharing of BioDiscovery research results.

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Computer assisted structure elucidation of natural products using two-dimensional NMR spectroscopy†

Cited by 59 publications

References 29 publications

Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation

Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation

Automated Interpretation of NMR Spectra for Small Organic Molecules in Solution

North-South BioDiscovery Research Collaboration of Indonesian Sponge and Soft Coral : A Bibliographic Analysis of Publications Over the Last Two Decades

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