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Search for "database" in Full Text gives 167 result(s) in Beilstein Journal of Organic Chemistry.
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
- colony of the UIAU-6B strain was purified by repeated subculture on pseudomonas agar base plates. The strain was identified by analysis of the molecular DNA sequencing of its 16S rDNA and the sequence obtained was compared with the Genbank database using the BLAST search of the National Center for
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
- pathways is largely unknown. In this work, we performed data mining of TF–glycogene relationships from the Cistrome Cancer database (DB), which integrates chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq data to constitute regulatory relationships. In total, we observed 22,654 potentially
- include: i) data from the Gene Transcription Regulatory Database (GTRD) [40], which has analyzed publicly available ChIP-Seq data with multiple algorithms to systematically catalog TF–gene relationships across several organisms and cellular contexts; ii) the Regulatory Circuits DB [41], which relies on
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
- , Weiterstadt, Germany). The obtained sequences were aligned using Geneious 6.0.5 [84] and compared to the NCBI sequence database [85] (Supporting Information File 1, Table S1). In case of isolates with multiple 99–100 % identity hits on several species within the same genus, we identified these only to the
- mature black poplar (Populus nigra) trees.a Volatiles emitted from endophytic fungi growing in culture on potato dextrose agar (PDA).a Supporting Information Supporting Information File 134: Sequences of isolated endophytic fungi and identification according to NCBI database, primer used in this study
Breaking paracyclophane: the unexpected formation of non-symmetric disubstituted nitro[2.2]metaparacyclophanes
Beilstein J. Org. Chem. 2021, 17, 1518–1526, doi:10.3762/bjoc.17.109
- chemistry can produce any substitution pattern there are few unsymmetrical [2.2]metaparacyclophanes (3) and only one X-ray crystallographic structure found in the CCDC database, and this is a triple-layered cyclophane [44]. We have been interested in the formation of substituted [2.2]paracyclophanes for a
A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry
Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91
- , and the relative amounts of the significant features were displayed as a boxplot. The selected significant features were further searched in the raw HRMS profiles to identify those with the reliable isotopic pattern assigned to a metabolite. The m/z values were searched in the METLIN database, using a
Structural effects of meso-halogenation on porphyrins
Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88
- the crystallographic structural characteristics of 13 mesox-halo-substituted porphyrins. Data obtained from the CSD crystal structure database accompanied by data obtained from our group are discussed [25]. Furthermore, any general structural motif that appears consistent among the mesox-halo
- -substituted porphyrins In the CSD database, there are a few other notable examples which whilst they are interesting, they do not constitute a significant library to support a complete discussion (compounds 20–24, Figure 21) [37][38][39]. Other examples do exist in the CSD, such as strapped systems [40], but
Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams
Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12
- groups are omitted for clarity. Full crystallographic data available in Supporting Information File 2 and Supporting Information File 3, and in Cambridge Crystallographic Database under CCDC-2001373 and CCDC-2001372 numbers, respectively. Proposed structures of compounds 5a and 2-epi-5a with 1H-1H
Molecular basis for protein–protein interactions
Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1
- complexes, with most of the complexes being homooligomeric complexes [58]. In fact, an analysis done in the BRENDA enzyme database [59] shows that there are more homooligomeric complexes than expected [60]. PPIs in homooligomeric complexes are usually difficult to predict using computational measures
- for illustration is the heterodimer of human NAD-dependent isocitrate dehydrogenase (Protein Database (PDB): 6KDF) [10]. Figure adapted from Carter et al. [11]. Mechanisms of homooligomeric complex formations. a) Domain swapping of RNase A (PDB: 1A2W) [73]. The swapped regions are shown in red. b
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
- its glycopeptide coverage. Those glycans were only present in low abundance on the glycopeptides, and often no MS/MS spectrum was present (Figure 3). However, it highlights the importance of a complete glycan composition list for a database-based identification of glycopeptides, something that is less
- database including 71,591 protein sequences (20,205 from Swiss-Prot and 51,386 from TrEMBL). The C-terminal cleavage of lysine and arginine and a maximum of two missed cleavages was allowed. A tolerance of 10 ppm was applied for the precursors and 20 ppm for fragment ions. A carbamidomethylation was set as
- a fixed modification for cysteine residues. Methionine oxidation was enabled as a variable modification. The search for N- and O-glycopeptides was separately performed. For this purpose, either the database “N-glycan 309 mammalian no sodium” (Supporting Information File 7) or “O-glycan 78 mammalian
Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities
Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248
- reads were assigned to the respective samples with an average of 12,083 reads per sample (range: 751 to 34,802; Table S3, Supporting Information File 1). The 16S rRNA reference sequences with a 99% identity criterion obtained from the SILVA database release 132 were trimmed to the V3-V4 region, bound by
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215
- specification of Linear Code to reaction rules, we aim to minimize inconsistent symbology thereby making glycan database queries easier. With a clear guide for generating reaction rule descriptions, glycan synthesis models will be more interoperable and reproducible thereby moving glycoinformatics closer to
- in database queries. Both GlycoCT and WURCS produce unambiguous representations and are thereby invaluable for many applications, ranging from systems biology analyses [17] to an international glycan structure repository [26][27][28][29]. GlycoCT and WURCS provide a high degree of unambiguous detail
- -glycan database called UniCorn, based upon a Perl implementation of reactions on glycans represented in Linear Code [37]. Though Linear Code is computer-parsable, there is still substantial work necessary to implement that parsing because there is no standard representation for handling the wide variety
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- distributed together with Privateer. If the existence of a glycan in the database is confirmed, then the software can attempt to find records about the sequence on other, more specialised databases (currently only GlyConnect) to obtain information such as the source organism, the type of glycosylation and the
- structures. Importantly, the majority of the glycan chains that do have a unique GlyTouCan accession ID assigned (except for single residues linked to protein backbones), have also been successfully matched on the GlyConnect database (Table 2). Results Examples of use As observed in previous studies
- might not necessarily be experts in structural glycobiology. The fact that these glycans could not be matched to standard database entries should be enough to raise the question with depositors, and at the very least write a caveat on a deposited entry where glycans could not be correctly identified
Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction
Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200
- the most likely conformations to correlate with experimental log P, one can assess the dependence of log P with molecular conformation. Accordingly, a consistent set of fluorine-containing agrochemicals (Figure 4) with experimentally available log P data was selected from a single database [24], which
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
- interface for generating carbohydrate structures to query the database included in GlyCosmos: GlyTouCan [34]. GlyCosmos is a web portal that integrates resources linking glycosciences with life sciences. Besides elements such as “SugarDrawer” and GlyTouCan (carbohydrate database), the platform GlyCosmos
- can be further used to search the GlyTouCan [34] database to explore the literature details related to the input structure. GlycoGlyph is an efficient tool for sketching or building glycans with a highly usable interface that can significantly help researchers to improve the uniformity in glycan
- notations for the University of Oxford (UOXF) format. The input complies with various linear sequence and text formats. They include GlycoCT, GLYcan structural Data Exchange using Connection Tables (GLYDE-II), Bacterial Carbohydrate Structures DataBase (BCSDB) [41], carbohydrate sequence markup language
Tools for generating and analyzing glycan microarray data
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
- version published in June 2016 can be found at: https://www.beilstein-institut.de/download/1458/mirage_glycan_array_guidelines_version_1.0__22_june_2016.pdf. Tools for glycan microarray data A) Repositories of glycan microarray data 1. CFG Database: Status: Available. Address: http
- ://www.functionalglycomics.org/glycomics/publicdata/primaryscreen.jsp. Description: The Consortium for Functional Glycomics (CFG) database of glycan array data (Figure 3A) is one of the largest archival resources for glycan microarray data. The CFG was founded in 2001 and was funded for about 10 years, during which time the
- main website and database were created [33]. The microarray work was then taken over by the National Center for Functional Glycomics (NCFG) which was established in 2013. The CFG database has over 3000 experimental results files with 2 major types of arrays, the mammalian glycan printed array (noted as
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
- DDA files (n = 12) downloaded from a previously published dataset [20] obtained from the ProteomeXchange Consortium via the MassIVE repository (PXD003369, MSV000079426). Two searches were conducted on each file, one N-linked and one O-linked. A human protein database was used (UniProt UP000005640
- peptide. For N-linked searches (N-X-S/T) a database of 164 N-glycans was used (Supporting Information File 1, Table S41) and for the O-linked searches (at any S/T) a database of 49 O-glycans (Supporting Information File 1, Table S42) was used. All glycan modifications were set as “Rare 1” allowing each
- included, parsed from the online UniProtKB database using an inhouse Python library. Statistical analyses Significant differences in glycoform abundances between healthy and diseased samples were evaluated using an unpaired two-tailed t-test without corrections for multiple comparisons. Missing values were
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
- based on a triple standard GU calculation [10][11] and database matching whilst the quantitation used HappyTools calibration and area calculation [14]. The GU calculation involved standardizing the migration time of the peaks by generating a ‘virtual’ glucose unit (GU) ladder calculated using the
- bracketing standards in the electropherograms, the variation of GU values for glycan peaks generally were within a very small range (Figure 1A and 1B) allowing for consistent database matching against a GU CE database (APTS fluorescent labelled) [10]. HappyTools was used to calibrate the migration times of
- label). The UPLC-MS approach was used to characterize a commercial Anti-HER-2 reference standard (Section 4.3.4 from mentors) using the UNIFI software and GU/mass database (RFMS labelled) provided by Waters Corp [18]. Figure 5A shows that 14 glycans were identified in 13 UPLC peaks using UPLC-MS
Three new O-isocrotonyl-3-hydroxybutyric acid congeners produced by a sea anemone-derived marine bacterium of the genus Vibrio
Beilstein J. Org. Chem. 2020, 16, 1869–1874, doi:10.3762/bjoc.16.154
- , respectively (Figure 1). A database search identified the planar structure of 4 in a patent that described 5 (Figure 1) from marine obligate Vibrio sp. C-984 [9]. To determine the absolute configuration of C3 in 1–4, an anisotropy-based chiral analysis using a chiral derivatization reagent, phenylglycine
Models of necessity
Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137
- new is prioritized over fully investigating the known. This is exemplified by the fact that for many researchers, the most valuable search in a large chemical structure database is often one that retrieves (correctly) zero hits. Cheminformatics is an old discipline that preceded the current interest
Heterogeneous photocatalysis in flow chemical reactors
Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125
- this problem, which has led photocatalysis to become one of the most active areas of chemical research in recent years. A crude search of the Web of Science database for the term “Photocatalysis” shows the exponential growth of interest in this area since the 1990s, with almost 8000 publications on the
Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole
Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113
- interaction (2.5–3.4 Å and 2.79 Å) [58][59][62][66] according to the calculations and the X-ray calculated average taken from the Cambridge Structural Database (CSD) [76]. Interestingly, in the case of the reaction between diene 8j and 7c, where the diene does not have an N-benzyl group, the endo TS also
Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors
Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108
- ) database, which compares the molecular structure of test compounds vs a large training set of experimental bioactive or inactive compounds [21]. The results of the prediction are summarized as probability of activity (Pa) and probability of inactivity (Pi) values, both ranging from 0 to 1 (Figure 2), where
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
- ) and PubChem (NIH). Both focus on characterising drug-like molecules and providing information to the public domain. The former is a manually curated database of bioactive molecules, which aims to bring together chemical, bioactivity and genomic data to aid the translation of genomic information into
- effective new drugs [79]. The latter is an open database for researchers to upload scientific data, including biological results, so that others may use it [80]. Perhaps the biggest example of open source drug discovery in its pure form is the Open Source Malaria project [81][82]. This is a platform for
- that genomic clones were made freely available, enabling researchers to investigate genes of interest [101]. Furthermore, genetic and genomic information was rapidly distributed, in the form of the ACeDB database, initially via gopher, an early internet service, and later via WormBase [105][106]. These
A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium
Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97
- DSM 45348, using the AntiSMASH database [17], and identified in total 14 biosynthetic gene clusters for polyketides and non-ribosomal peptides. Intrigued by this, a strain available from the NBRC culture collections [18] was cultured and examined by HPLC–DAD analysis, which gave several peaks in the
- , which was chosen with the aid of a database survey on the history of chemical studies and the presence of biosynthetic genes. The same approach is also applicable to other natural product resources and should help discover metabolites with higher degree of novelty, provided that support from
Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition
Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59
- Biotek Synergy HTX multimodal plate reader after incubation for 30 minutes. Preparation of the HDAC8 receptor for docking The HDAC8 crystal structure (protein database pdb: 1W22) [32] was utilized as the docking receptor for all compounds. This receptor is crystalized as a dimer thus only the A chain was
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