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Search for "databases" in Full Text gives 63 result(s) in Beilstein Journal of Organic Chemistry.
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
Anthelmintic drug discovery: target identification, screening methods and the role of open science
Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105
- helminths, but that the rate of drug discovery has been very low, so efforts must be made to enhance cooperation among the various groups pursuing this strategy [83]. They go on to suggest that sharing of both positive and negative screening data via online databases is a priority to focus attention on the
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
A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA
Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100
- our SDFS on the sequence inside the first exon. Although splice variants of AR-FL (full-size molecule), AR-V7, and AR-V9 [17][18] are the most important ones from a clinical point of view, we analyzed all nucleotide sequences of the translated AR mRNAs from open databases (Supporting Information File
Opening up connectivity between documents, structures and bioactivity
Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54
- millions effectively burying these relationships in PDFs over many decades but must now spend millions more trying to get them back out. The key imperative for this is to increase the flow into structured open databases. The positive impacts will include expanded data mining opportunities for drug
- in minutes. Unfortunately, no journals have yet instigated a flow of author-specified DARCP directly into open databases. Progress may come from trends such as open science, open access (OA), findable, accessible, interoperable and reusable (FAIR), resource description framework (RDF) and WikiData
- . However, we will need to await the technical applicability in respect to DARCP capture to see if this opens up connectivity. Keywords: activity data; databases; drug discovery; chemical structures; protein targets; Introduction This article assesses a key aspect of data sharing that has the potential to
Isolation of fungi using the diffusion chamber device FIND technology
Beilstein J. Org. Chem. 2019, 15, 2191–2203, doi:10.3762/bjoc.15.216
- comparison (BLAST) of DNA sequences (ITS1, ITS2, 18S, 5.8S, 28S, RPBII, tef1α and β-tubulin) with reference sequences deposited in public databases (GenBank) and microscopical analysis of morphological characteristics, identified 12 ascomycetes from 12 different genera. Except for Scopulariopsis brevicaulis
Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum
Beilstein J. Org. Chem. 2019, 15, 789–794, doi:10.3762/bjoc.15.75
- was isolated and identified by one- and two dimensional NMR spectroscopy (Table S2, Supporting Information File 1), EIMS databases and GC retention index as the known sesquiterpene (Z)-γ-bisabolene (5). Because the two olefinic carbon atoms of its quaternary double bond could not be unambiguously
Back to the future: Why we need enzymology to build a synthetic metabolism of the future
Beilstein J. Org. Chem. 2019, 15, 551–557, doi:10.3762/bjoc.15.49
- million proteins were deposited into protein sequence databases, such as UniProtKB [29]. More than 40,000 enzymes were biochemically characterized and the corresponding data is available in specialized enzyme databases, such as BRENDA [30]. This wealth of biological information provides a good starting
- point to search for enzyme variants that possess a desired catalytic activity. While existing databases might provide a good resource to find the parts to reconstruct level 3 pathways, this task becomes more challenging in respect to level 4 and level 5 designs that require new-to-nature reactions. How
- protein sequence and enzyme databases for suitable candidates is key to advance metabolic retrosynthesis. However, there are still some practical issues in extracting the necessary information from different databases. One particular problem of sequence databases like UniProtKB is the high number of
Adhesion, forces and the stability of interfaces
Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12
N-Acylated amino acid methyl esters from marine Roseobacter group bacteria
Beilstein J. Org. Chem. 2018, 14, 2964–2973, doi:10.3762/bjoc.14.276
- spectra often reveal key structural features. Furthermore, the availability of large cross-platform databases useful for dereplication allows focussing on new compounds. We are interested in natural compounds from Roseobacter group bacteria, an abundant class of marine bacteria occurring in diverse
Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics
Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267
- form the binding pocket (Figure 4) [58][59]. Utilizing a virtual screening of two different databases (i.e., the National Cancer Institute [60] and an in-house collection of 32,000 compounds), Wijfells et al. were able to identify a small-molecule mimic of the des-amino-Leu-Phe (dLF) component of the
Volatiles from the tropical ascomycete Daldinia clavata (Hypoxylaceae, Xylariales)
Beilstein J. Org. Chem. 2018, 14, 135–147, doi:10.3762/bjoc.14.9
- significant activities against competing microbes, but the volatile profiles of these biocontrol candidates were only evaluated using databases like NIST, which can only serve to detect and identify known compounds. The current study demonstrates the need of chemical synthesis for rigorous identification of
Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes
Beilstein J. Org. Chem. 2017, 13, 2408–2415, doi:10.3762/bjoc.13.238
- that the Slf protein sequence might be a useful probe to uncover further examples of strains producing these or closely-related compounds. BLAST analysis of public databases using the protein sequence of the Slf of DSM4137 as a probe sequence uncovered multiple candidate Slf sequences (see sequence
- before or after the specific sulfonation step. The sequence of the sulfotransferase is a useful probe to uncover related gene clusters in public sequence databases. Sulfonation remains a rare and relatively poorly understood modification in natural product biosynthesis [27][28][29][30]. As our
Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system
Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88
- peptides from primary sequence databases with Mascot (http://www.matrixscience.com/). The biological function of recombinant proteins of mammalian origin expressed in insect cells may be altered by different N-glycan status. We observed that the terminal sialic acid residues are essential for the GABA
Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems
Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85
- databases and computational tools [73] that enable model-based optimization such as flux-balance analyses [74]. Taking advantage of natural presence and manipulability of distinct isoprenoid pathways in both organisms (MEP in E. coli and MEV in S. cerevisiae), heterologous production of several isoprenoid
- iceberg. Potentially, modular biosynthesis that has resources to fast expanding databases will widen the amenable targets for large scale production to unforeseen extend. As a prerequisite, strain optimization of heterologous hosts has to be developing with equal progress although continuous reporting
Computational methods in drug discovery
Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267
- resonance (EPR) spectroscopy data has also been used in high-resolution de novo structure prediction [75][76][77]. Protein and small molecule databases Information about drug molecules and target structures is critical in using SBDD tools and many repositories collect and store such information about small
- database which has non-redundant protein sequences which are manually annotated to contain descriptions such as functional information of protein sequences and post-translational modifications [84]. PDB and Swiss-Prot are both general purpose biological databases. There are other databases that contain
- databases. One limitation of this approach can be attributed to its high complexity. When a high-resolution target structure is available, ligand growing programs such as biochemical and organic model builder (BOMB) can be used to design ligands that bind to the target without using ligand databases [155
A new paradigm for designing ring construction strategies for green organic synthesis: implications for the discovery of multicomponent reactions to build molecules containing a single ring
Beilstein J. Org. Chem. 2016, 12, 2420–2442, doi:10.3762/bjoc.12.236
- ][111][112][113][114][115][116], and the creation of encoded synthesis databases that purportedly assist chemists in proposing optimum syntheses to known target molecules subject to constraints, notably number of steps, and cost and availability of commercially available starting materials [117][118
- pursued in a meaningful, targeted, and systematic fashion. However, the current structure of literature databases such as SciFinder or Reaxys do not allow for facilitated structure searches based on synthesis strategy maps. What would be needed is for a user to input a target heterocyclic structure
- This paper is dedicated to the memory of Professor Malcolm Bersohn who was a pioneer in developing computer databases to devise efficient organic syntheses at the University of Toronto.
The EIMS fragmentation mechanisms of the sesquiterpenes corvol ethers A and B, epi-cubebol and isodauc-8-en-11-ol
Beilstein J. Org. Chem. 2016, 12, 1380–1394, doi:10.3762/bjoc.12.132
- standard. Furthermore, various high quality databases containing the EI mass spectra and retention indices of thousands of compounds are available that assist in automated compound identification [2][3]. If unknown compounds are detected in natural extracts, their structure elucidation by GC–MS is more
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