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Search for "databases" in Full Text gives 54 result(s) in Beilstein Journal of Organic Chemistry.
Monitoring carbohydrate 3D structure quality with the Privateer database
Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83
- new resources, including services and databases [9][10][11][12][13], and standalone software [14][15][16][17][18]. Among these, the Privateer software package has been a key tool for glycoprotein and protein–carbohydrate complex validation: Privateer analyses the conformational plausibility of each
- sugar model [3], checks that structures match the nomenclature used for deposition in the PDB [14], compares glycan compositions to known structures as reported by glycomics (e.g., GlyConnect [19]) and glyco-informatics (e.g., GlyTouCan [20]) databases and repositories [15], and checks how close the
- validation report entry in plaintext can be difficult, time-consuming and would certainly be a poor experience for the end user. To improve the utility of this database, we have provided a visualisation of the information contained within the validation report for both PDB and PDB-REDO databases, which is
Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria
Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75
- have previously identified several Vs NnlA homologs in sequence databases [20], however, the NNG degradation activities of these homologs have not been tested. Doing so will differentiate between these two hypotheses by testing if NnlA homologs with NNG degradation activity are highly conserved or if
Introduction of a human- and keyboard-friendly N-glycan nomenclature
Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53
- suggests that such an endeavor could well be of practical importance. Developed to be a human and keyboard-friendly alternative to machine codes, the proglycan code nevertheless qualifies as a valuable component of glycan databases. A simple text search can retrieve all N-glycan structures with a
Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin
Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31
- member of characterized melon lectins, namely the Cucumis melo agglutinin (CMA1), an R-type lectin derived from melon. Prior to our study, CMA1 was only a predicted protein from genomic sequencing, with moderate certainty scores on lectin-specific databases. Our comprehensive analysis using glycan array
NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform
Beilstein J. Org. Chem. 2024, 20, 25–31, doi:10.3762/bjoc.20.4
- of NMR data. While initially intended for small molecules data repositories and databases [34][35], NMRium provides unique functionalities that make it particularly well-suited for educational application. Teaching the interpretation of NMR spectra Nowadays, the interpretation of NMR experiments is
GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data
Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134
- molecules" (that is, previously referenced in databases) is expected to be significant compared to unknown ones, it is important to make sure that the model is discriminative and we want to maximize the precision of the model at this task. Indeed, the large amount of positive results would make it difficult
Navigating and expanding the roadmap of natural product genome mining tools
Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178
- used to search in NP databases for identical or related compounds [18][19]. While the BGC-centric approach might be more accurate, it is limited by the number of characterized BGCs in publicly available databases. Since significantly more NPs than NP BGCs are characterized, the search space of known
- ][44][45][46]. The advantage of such reference alignment methods that are based on sequence homology is their high confidence. The performance of these tools can be rapidly improved via the addition of new reference databases, which was contributing to their success at the beginning of the genome
- associated NP [56][57][58]. In silico dereplication to eliminate BGCs associated with known NPs is one of the major functions of genome mining to avoid the time-consuming and costly re-isolation of known NPs. For instance, the antiSMASH platform compares putative BGCs with reference databases to detect BGCs
Efficient production of clerodane and ent-kaurane diterpenes through truncated artificial pathways in Escherichia coli
Beilstein J. Org. Chem. 2022, 18, 881–888, doi:10.3762/bjoc.18.89
- , as well as two possible producers (Streptomyces sp. San01 and Kitasatospora sp. CB02891) after a survey of the existing genome sequence databases, however, we discovered a strain, Kitasatosporia griseola DSM 43859, without a genome sequence disclosed, from the strain library of CGMCC. Using the
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- tightly connected to mainstream bioinformatics. For example, databases and tools from genomics can be used for gaining information about genes encoding for glycosyltransferases, glycosidases, and glycan-binding proteins (lectins), and search engines initially designed for the detection of
- development and evolution of dedicated databases that store glyco-related quality information. With glycobioinformatics still being in its infancy, these requirements are continuing to evolve. The editors of this thematic issue represent both bioinformatics developers as well as users who have the conviction
- be detected when comparing similar glycomes by this method. The articles by Groth et al. [12] and by Bagdonas et al. [13] illustrate how glycoinformation can be harvested and integrated from available -omics databases, with the former paper identifying putative cell signaling molecules and
Isolation and characterization of new phenolic siderophores with antimicrobial properties from Pseudomonas sp. UIAU-6B
Beilstein J. Org. Chem. 2021, 17, 2390–2398, doi:10.3762/bjoc.17.156
- methanolic extract from a small-scale culture of Pseudomonas sp. UIAU-6B in modified SGG medium indicated the presence of some interesting peaks with molecular ions which gave no hits when they were searched in natural product databases (Antibase). At the same time, the 1H NMR fingerprints suggested the
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis
Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119
- , but enhancers present several kilobases away from the transcription state site (TSS) are neglected; and iii) most of these reported TF–glycogene relationships only have partial support in established bioinformatics databases (DBs, see Supporting Information File 1). Thus, these are limited hypothesis
Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves
Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118
- volatiles were identified by comparing their mass spectra with those of authentic standards or reference spectra from databases (Wiley, Version 8, National Institute of Standards and Technology (NIST, Version 11)) using GCMS SOLUTION v.4.20 (Shimadzu). In addition, non-isothermal Kovats retention indices
Breakdown of 3-(allylsulfonio)propanoates in bacteria from the Roseobacter group yields garlic oil constituents
Beilstein J. Org. Chem. 2021, 17, 569–580, doi:10.3762/bjoc.17.51
- suggests that the deallylation of AllMSP by the DmdA variants in these organisms may be less efficient than was observed for P. inhibens. Besides these sulfur compounds, only O. indolifex, but not the other two strains, released another compound, 27, whose mass spectrum was not included in our databases
Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases
Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30
- enzyme-encoding sequences, filling up databases with a wealth of information. However, while resolving an early step in the discovery pipeline, these techniques progressively create a new bottleneck regarding enzyme characterization. Therefore, there is a pressing need to extend the enzymologist’s
Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils
Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11
- viscosities of 40 °C and 100 °C are used to calculate the VI, using databases like viscosity index calculators of Evonik [32]. While the VI of Nynas NS8 was increased by 100% (VI 47 to 94) using compound 2, compound 4 was able to increase its VI by 89% (VI 47 to 89). In contrast to that, the VI of Nexbase
Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification
Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253
- quantification. Importantly, LaCyTools requires RT clusters to be defined in which MS1 spectra can be summed and further processed, which is facilitated by the GlycopeptideGraphMS output. The analyte list may be extended by including glycan compositions (e.g., from the literature or databases such as GlyConnect
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve
- knowledge are bioinformatics databases that have been curated through the deposition of experimental data. Bioinformatics databases contain detailed descriptions of the glycan compositions and m/z values of specific glycans, and therefore aiding the process of glycan annotation [47]. Such bioinformatics
- databases can usually be interrogated using textual or graphical notations that describe the glycan sequence. However, due to the glycan complexity and the incremental nature of the different glycomics projects, numerous notations have been developed over the years – e.g., CarbBank [48] utilized CCSD [48
Computational tools for drawing, building and displaying carbohydrates: a visual guide
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
- several computer applications using a standardised notation. The earliest glycan editors allowed manual drawing similar to ChemDraw or used input files with glycan sequence KCF (KEGG Chemical Function) [9] in text format for similarity search against other structures deposited in the databases. Later
- glycoscience research, we have identified the tools and databases that are freely available on the internet and are regularly updated and improved [1]. The variety and complexity of glycan structures make their interpretation challenging. Consequently, in the past few years, several sketching, building and
- computational tools was inspected for general features related to sketching, representing and model building, all of which could be further used as input for translation into other formats, search from glycan databases or complex calculations such as molecular simulations. Several tools feature an interactive
A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study
Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196
- data collection databases for all commodity material resources, and so this significant limitation prevents estimation of time analyses pertaining to how long a given resource may exist under a so-called “sustainability condition”. For first generation chemical feedstocks arising from fossil fuels, the
- necessarily requires reliable databases that constantly track data annually. Such tracking is not always in industry’s best interest to disclose such information publicly for economic and political reasons. For example, providing inaccurate or incomplete information to governments and investors can leverage
- -derived materials. In any event, the task of tracing starting materials, catalysts, and reaction solvent syntheses is very tedious, especially for time-pressed chemists who wish to practice green chemistry. However, such a task can be significantly alleviated if synthesis databases of first, second, and
Tools for generating and analyzing glycan microarray data
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
- predicts if the protein will be able to bind them. The current limitation is that it has data only from the CFG database. Thus, building glycan array databases which are easily accessible to multiple tools can further improve the development of tools like this and help grow a field of predictive
- to use depending on glycoconjugate and linker type, and scanning requirements. These linker types and surfaces are the most commonly used and there are more specialized surfaces and linker chemistries that are commercially available. Screenshot of microarray databases: (A) Screenshot of an example of
GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis
Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180
- packages have been developed for analysis of outputs from MS technology to automate the process of transformation of raw MS data into ion intensities and matching them with appropriate glycan and peptide sequence databases for glycopeptide identification (reviewed in [12][13][14][15][16]). However, there
Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations
Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176
- available GU-based glycan databases [11][12][13]. The technique is suitable for the assessment of glycosimilarity of biologics [14] and most importantly has potential for analyzing large cohort studies to assess the aforementioned process parameters and their correlations with antibody glycosylation [7]. GU
- databases and software (among others) are discussed in a recent review [15]. A long standing problem associated with the analysis of large sets of electrophoretic data generated during bioprocessing is inevitably the drift of the peak migration time and area under the curve pertaining to glycan structures
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
- micro- (or macro-)heterogeneity of glycan sequences at specific sites [7]. These complexities are very difficult to resolve, requiring high levels of expertise and multi-layered orthogonal approaches [7][8][9][10]. Within this framework, the contribution of glycoinformatics tools and databases
Models of necessity
Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137
- molecules suitable for depiction in databases, cheminformatics, machine learning (ML) or artificial intelligence (AI): It is essential for chemists to be able to communicate with each other about molecules. The language of chemistry varies slightly between the organic and inorganic communities. However, it
- ] describes this situation as using a so-called folk ontology (the everyday language of chemistry) as a fiction when discussing a very complex mathematical model (quantum mechanics). The third ontology, and the one that interests us most here, is how we describe molecules to computers for building databases
- searching of reactions in chemical databases, based on connectivity of atoms has become a very useful tool for the synthetic chemist. We have mentioned one limit above; that the Woodward–Hoffmann orbital-based rules are necessary to describe electrocyclic reactions [29]. Reaction databases that only store
Activated carbon as catalyst support: precursors, preparation, modification and characterization
Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104
- phosphorous species in the carbons could be responsible for the examined difference [130]. X-ray diffraction (XRD): X-ray diffraction gives information on the crystallinity or amorphicity of activated carbons. Comparison of resulting XRD patterns with the crystallographic databases clarify that partially
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