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Search for "database" in Full Text gives 167 result(s) in Beilstein Journal of Organic Chemistry.
Opening up connectivity between documents, structures and bioactivity
Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54
- results. But isn’t there enough of this out there already? This can be answered in two parts. The first is that a conservative estimate of the capture backlog would be at least two-fold more data still entombed in PDFs that is not currently indexed in database records. The second part is the imperative to
- getting the structures “back out” for database capture needs either manual re-sketching or use of an image-to-structure (i2s) tool such as optical structure recognition (OSRA) [6], both of which are error-prone processes. The common practice of including tables of Markush representations, while they
- leading commercial sources that capture DARCLP at scale are the Global Online Structure Activity Relationship Database (GOSTAR) [15] from Excelra (formerly GV000Bio) and Elsevier Reaxys Medicinal Chemistry [16]. The current statistics for these are shown in Table 1. The GOSTAR numbers have a more detailed
Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0
Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40
- application [66]. Data collection [67] in combination with self-leaning software related to artificial intelligence (A.I.) drives their use in applications with more efficiency in large workflows. Such tools can recognize failures in industrial processes just by collection of data in a big database where data
Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds
Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22
- in organic molecules [30][31]. Early reports by Glusker and co-workers in 1983 and 1994 showed C–F···H interactions in structures found in the Cambridge Crystallographic Data Centre database [32]. Similar evidence was reported by Howard, O’Hagan, Desiraju and their co-workers where the C–F···H
Two new aromatic polyketides from a sponge-derived Fusarium
Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289
- database. HPLC/UV-guided purification of the secondary metabolites from this strain led to the isolation of two new polyketides, karimunones A (1) and B (2), together with five known compounds (3–7, Figure 1). Compound 1 was obtained as a red powder. TOF-HRESIMS analysis gave a deprotonated molecule [M − H
Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering
Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283
- (BGCs). While the antiSMASH database (online repository of BGCs predicted by the genome mining platform antiSMASH) lists more than 4,000 bacterial terpene BGCs [43], only 127 have been characterized and deposited in the MIBiG database (repository of characterized BGCs) to date (Figure 3) [44]. The
Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum
Beilstein J. Org. Chem. 2019, 15, 2872–2880, doi:10.3762/bjoc.15.281
- (Supporting Information File 1, Figure S2). Relatedness of PpolyTPSs to the TPSs from dictyostelid social amoebae, fungi, and bacteria When individual PpolyTPS genes were used as query to search against the nonredundant protein database at NCBI, the top hits for PpolyTPS2 and PpolyTPS3 were all from bacteria
- the Physarum polycephalum Genome Resources database (http://www.physarum-blast.ovgu.de). Protein sequences were predicated using TransDecoder (5.0.2) [37]. Putative terpene genes were searched against SmMTPSLs HMM profile [38] using HMMER 3.0 hmmsearch [39] with an E-value of 1e−5. The coding region
- alignment of the protein sequences of the four PpolyTPSs. The sequences for PpolyTPS1-PpolyTPS4 reported in this paper have been deposited in the GenBank database (accession numbers. MN523652–MN523655). Three signature motifs for terpene synthases were boxed. Shadings in black and gray indicate identical
Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis
Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256
- the AAFTF pipeline (https://github.com/stajichlab/AAFTF). To facilitate the identification of a putative biosynthetic gene cluster, a local BLAST database was created from the resulting assembly [44]. Though Shinohara et al. list the revised annotation of AstC as AORIB40_05408, its amino acid sequence
- clusterblaster (https://github.com/gamcil/clusterblaster). A DIAMOND [47] database was built from protein sequences extracted from these genomes, and clusterblaster was used to rapidly identify biosynthetic gene cluster homologs in A. ustus and A. calidoustus. Genomes for A. insuetus CBS 107.25 and A
Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp.
Beilstein J. Org. Chem. 2019, 15, 2327–2332, doi:10.3762/bjoc.15.225
- second report on the small molecule from this underexplored taxon. According to the genome sequence database, biosynthetic genes for NRPS and siderophore are present in Microbulbifer species which will be pursued in our future investigation. Experimental General experimental procedures The UV spectrum
Isolation of fungi using the diffusion chamber device FIND technology
Beilstein J. Org. Chem. 2019, 15, 2191–2203, doi:10.3762/bjoc.15.216
- obtained by four FIND experiments and identified by sequence comparison with the best BLASTn match within the NCBI GenBank database. Supporting Information Supporting Information File 184: Genomic sequences of isolated fungi, data on bioactivity and halotolerance, spectroscopic data of compounds 1 and 2
Genome mining in Trichoderma viride J1-030: discovery and identification of novel sesquiterpene synthase and its products
Beilstein J. Org. Chem. 2019, 15, 2052–2058, doi:10.3762/bjoc.15.202
- prediction of the potential terpene synthases in J1-030 genome, gene Tvi09626 was selected and the following bioinformatics analysis of the function of this unidentified terpene synthase was performed. A protein blast search against the NCBI database was performed with Tvi09626, revealing sequence identities
Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)
Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190
- mass spectra with those of the NIST database (when available), taking into account the match factors and reverse match factors. A series of n-alkanes (C7–C30) were analyzed. The retention times of the measured n-alkanes on the first GC column were used to calculate the retention indices I according to
Phylogenomic analyses and distribution of terpene synthases among Streptomyces
Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115
- available in the NCBI database and compared the distribution of terpene synthase genes among them. Furthermore, we studied whether phylogenetic trees calculated based on the three most abundant terpene synthases in Streptomyces represent the evolution of the Streptomyces species based on the whole genome
- selected to construct a whole genome-based phylogenetic tree (Figure 1). The NCBI database was accessed on September 30th 2018. An orthologues-based approach was adopted to generate a species tree using OrthoFinder. OrthoFinder resulted in a total of 19980 orthologue groups (Table S1, Supporting
- interaction with their environment is highly desired. Experimental Streptomyces genomes selection Genomes with whole sequences available in the NCBI database (thus not partial sequences) were included. Custom shell scripts (https://github.com/kumarsaurabh20/distribution_of_terpene_synthases) were used to
New terpenoids from the fermentation broth of the edible mushroom Cyclocybe aegerita
Beilstein J. Org. Chem. 2019, 15, 1000–1007, doi:10.3762/bjoc.15.98
- m/z 519.2718 in the HRESIMS spectrum. 1H and 1H,13C-HSQC NMR data (Table 1) indicated the presence of four methyls and twelve methylenes, three of them oxomethylene groups. A database search with this data within the Chapman & Hall Dictionary of Natural Products on DVD suggested its identity as
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
- essential to identify suitable candidate templates to engineer or evolve a new activity within the backbone of a given enzyme. For example, although the BRENDA database is probably one of the best resources to learn about the detailed catalytic properties of enzymes, it only provides in selected cases
Volatiles from the hypoxylaceous fungi Hypoxylon griseobrunneum and Hypoxylon macrocarpum
Beilstein J. Org. Chem. 2018, 14, 2974–2990, doi:10.3762/bjoc.14.277
- identification requires a good match of the recorded electron impact (EI) mass spectrum to a database spectrum and of the retention index, a standardised GC retention factor that is calculated from the retention times of the analytes and of n-alkanes [15], in comparison to an authentic standard or published data
- exhibited the mass spectra shown in Figure 4E and Figure 4F that were similar to database spectra of 2,5-dimethyl-p-anisaldehyde (25) and methyl 2,5-dimethyl-p-anisate (26). The substitution pattern of these compounds is well explained by polyketide biosynthesis logic (Scheme 3). Starting from ACP-bound
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
- database [82] was searched for structurally similar compounds leading to the identification of the meta-substituted tetrazole 33 (Figure 7), which was found to have a similar dissociation constant. Moreover, in order to predict the orientation of the fragments in the binding site, molecular docking of 33
Synthesis of mono-functionalized S-diazocines via intramolecular Baeyer–Mills reactions
Beilstein J. Org. Chem. 2018, 14, 2799–2804, doi:10.3762/bjoc.14.257
- -functionalized S-diazocine 3 single crystals could be obtained, which were characterized by single crystal X-ray diffraction. The structure of 3 is the first crystal structure of a S-diazocine reported in the Cambridge Structural Database (CSD; version 5.39; Feb. 2018) [28]. This compound crystallizes in the
Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections
Beilstein J. Org. Chem. 2018, 14, 2607–2617, doi:10.3762/bjoc.14.239
- pubmed.gov database yields 292 references on the topic (as of 06/08/2018), with an exponential increase over the years. Unfortunately, as the terms ‘antivirulence’ and ‘pathoblocker’ are often used interchangeably, many publications in the field are not found in this type of search, for example the
Chiral bisoxazoline ligands designed to stabilize bimetallic complexes
Beilstein J. Org. Chem. 2018, 14, 2002–2011, doi:10.3762/bjoc.14.175
- coordination geometry and the bridging μ2-Br atom. The Ni∙∙∙Ni in 25·Ni2(OAc) at 4.176 Å is longer due to its longer three-atom bridge from OAc. In the Cambridge Structural Database (CSD), there are ten instances of Ni–N–N–Ni bond connectivity with sp2 N-atoms that are also bonded to a C-atom. However, all of
Natural and redesigned wasp venom peptides with selective antitumoral activity
Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144
- ][7][8], and fungi [1][9][10], they can kill cancer cells [11]. So far, >2,500 AMPs have been described in the literature and only ≈10% of those are known to exhibit anticancer activity, according to the Antimicrobial Peptide Database (http://aps.unmc.edu/AP/main.php). In total, there are around 600
- anticancer/antitumoral peptides according to the Database of Anticancer Peptides and Proteins (http://crdd.osdd.net/raghava/cancerppd/). Those AMPs with anticancer activity have been termed anticancer peptides (ACPs). Since their initial discovery, ACPs have constituted a promising alternative to
Two new 2-alkylquinolones, inhibitory to the fish skin ulcer pathogen Tenacibaculum maritimum, produced by a rhizobacterium of the genus Burkholderia sp.
Beilstein J. Org. Chem. 2018, 14, 1446–1451, doi:10.3762/bjoc.14.122
- -aminoacrylonitrile, and thioimidazolinone [10], all of which are not preceded in metabolites from other taxa. The large genome size of Burkholderia also suggests a high capacity for secondary metabolism. According to the NCBI genome database (https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/), the genome
Volatiles from three genome sequenced fungi from the genus Aspergillus
Beilstein J. Org. Chem. 2018, 14, 900–910, doi:10.3762/bjoc.14.77
- rich secondary metabolism with 807 compounds from 675 species that were recently summarised in the Aspergillus secondary metabolome database [14]. However, only a few studies about volatile natural products from Aspergillus are available [15][16][17][18][19][20][21][22]. Here we report on the volatiles
- tentatively identified as (Z)-octa-1,5-dien-3-ol (2) from its mass spectrum (Table 1 and Scheme 1A). Unfortunately, a retention index for 2 is not available from the literature, but the mass spectral database hit was very good and the assigned structure for 2 is biosynthetically reasonable: For compound 1 a
Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies
Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69
- in the case that one of the cell dimensions is more than 17 Å the two others being also about 15.5 Å. The Cambridge Structural Database (CSD) [32] search resulted in 26 structures of inclusion compounds in β-CD with similar cell dimensions. Among them, three entries (ANAXAP [33], UJEFEV [34] and
Volatiles from the xylarialean fungus Hypoxylon invadens
Beilstein J. Org. Chem. 2018, 14, 734–746, doi:10.3762/bjoc.14.62
- compounds (11, Figure 4A) suggested the structure of a dimethylphenol, but the mass spectra of several regioisomers in our database proved to be nearly identical. The measured retention index (I = 1152) matched with a published retention index for 2,5-dimethylphenol (I = 1151) [15], but retention indices
Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review
Beilstein J. Org. Chem. 2018, 14, 470–483, doi:10.3762/bjoc.14.33
- Reference sequence (RefSeq) database at NCBI [73] typing “7-alpha-hydroxysteroid dehydrogenase”. 7β-Hydroxysteroid dehydrogenases (7β-HSDH) Unlike their homologues, only few examples of bioconversion with 7β-HSDH have been reported in literature (Table 3, [33][65][74][75][76][77], Figure 5): one NADP
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