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Search for "prediction" in Full Text gives 151 result(s) in Beilstein Journal of Organic Chemistry.
Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling
Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144
- explanation and prediction of GAG specificity [35]. Computational methodologies like molecular docking and molecular dynamics (MD) have proven to be successful in modelling protein–GAG interactions, particularly examining the fundamental questions related to these interactions such as their specificity, the
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
- GalN as well as 8 other molecules. For benchmarking purposes, all spectra were annotated with true labels. By running the model inference for one spectrum multiple times we can measure the variability of its prediction probability for each category. If the model gives consistently a high probability
- the classification categories. We ran model inference 200 times on each sample and obtained the mean prediction probability for every category as its variability represented by the interpercentile range 5 to 95%. The results are shown in Figure 5. As an example: the spectrum of CS-C is predicted as
- GlcNAc with 95% probability in average but for 10 inferences out of 200 (the lowest 5% percentile) the prediction probability is below 60%. In this example, by thresholding on the interpercentile range below 0.35 for the most likely prediction of each spectrum one can obtain a precision of 100%. Most
A novel recyclable organocatalyst for the gram-scale enantioselective synthesis of (S)-baclofen
Beilstein J. Org. Chem. 2023, 19, 1811–1824, doi:10.3762/bjoc.19.133
- . MarvinSketch was used for logP prediction, MarvinSketch 20.11, ChemAxon (https://www.chemaxon.com). Demethylated cinchona squaramide 6 The demethylated cinchona squaramide was prepared according to the literature procedure [39]. To the best of our knowledge, the NMR assignment has not been reported yet. 1H NMR
Functional characterisation of twelve terpene synthases from actinobacteria
Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100
- for a pathway reconstruction towards artemisinin. The increased knowledge about terpene synthases together with the structures of their products will also be of interest for machine learning approaches to enable the prediction of terpene synthase functions from their amino acid sequences. Both aspects
Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements
Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184
- kneading enabled prediction of their space groups based on their isostructurality with known reference complexes. Comparison of these experimental patterns with simulated PXRD patterns based on SCXRD data revealed that the single crystals obtained by co-precipitation were isostructural with their
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
- with their substrate specificity [27]. This correlation can be used for the prediction of trans-AT PKS-derived polyketide core structures and is referred to as the correlation rule [19]. All commonly occurring domains in assembly line-like NP biosynthetic pathways as well as their non-modular homologs
- using current bioinformatic approaches (Figure 3E (e.g., kojic acid (11) [36])). Therefore, the prediction of these BGCs is mainly based on the co-localization of adjacent genes encoding tailoring or additional core enzymes. The current BGC prediction approach has its limitations, as genes involved in
- rely on alignments of annotated open reading frames (ORFs). Yet, their purpose, functions, and additional features such as comparative analyses of BGCs, dereplication concepts, or NP structure prediction differ significantly. In addition, some tools implement alternative BGC identification methods like
Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups
Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137
- prediction of two C2 related, dominating binding sites on 14-3-3ζ that may bind to two of the supramolecular ligand molecules. Keywords: AIE luminophores; fluorescence emission; guanidiniocarbonyl-pyrrole; ligand binding; 14-3-3 protein; Introduction The 14-3-3 protein family was one of the first
- ). Furthermore, we discovered that two ligands 1 simultaneously bind to one 14-3-3ζ dimer as determined by a fluorescence titration using the Job’s method (Supporting Information File 1, Figure S29 [29]). This experimental result is consistent with our computational prediction that 1 has two high-affinity
Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants
Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135
- combination with ground-breaking machine learning approaches for protein structure prediction such as AlphaFold2 [108], we anticipate that the catalytic repertoire of CYPs will be exploited much more for the biotechnological production of tailor-made triterpenoids and steroids in the near future. We hope that
Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions
Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134
- before, the theoretical prediction procedure represented in Figure 5b ignores the presence of polyP in the reaction mixture. However, in the reaction also polyPn and polyPn−1 take part; their concentration ratio might additionally influence the equilibrium position of the overall reaction. As it is not
New azodyrecins identified by a genome mining-directed reactivity-based screening
Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102
- the prediction of the producer of natural products with the functional groups of interest, leading to a higher rate of hits. We recently exploited genome mining targeting hydrazine synthetase and the generation of inorganic hydrazine N2H4 in acid hydrolysate as an indicator of N–N bond-containing
- was incubated with recombinant Ady1 in the presence of SAM, it was converted to 8, showing that Ady1 can install the methyl ester of azodyrecins (Figure 4). The in vitro characterization of Ady1 and the functional annotation of ady clusters allowed the prediction of the entire biosynthetic pathway of
Regioselectivity of the SEAr-based cyclizations and SEAr-terminated annulations of 3,5-unsubstituted, 4-substituted indoles
Beilstein J. Org. Chem. 2022, 18, 293–302, doi:10.3762/bjoc.18.33
- , some trends in the prediction of site of ring-closure can be derived. In general, absence of an electron-donating group in the indole benzene ring promotes C3 regioselective cyclization, provided the size of the newly formed ring is greater than six. Under the opposite scenario, C5 regioselective
DABCO-promoted photocatalytic C–H functionalization of aldehydes
Beilstein J. Org. Chem. 2021, 17, 2959–2967, doi:10.3762/bjoc.17.205
- Information File 1 for more details.) The experimental results with DABCO show that the prediction of a mildly endergonic HAT reaction step and the presence of a barrier are not an obstacle to its ability to act as a catalyst. A naïve use of BDE analysis to select HAT catalysts might suggest that DABCO should
Strategies for the synthesis of brevipolides
Beilstein J. Org. Chem. 2021, 17, 2399–2416, doi:10.3762/bjoc.17.157
- . Analysis of data combination from ovicidal activity, mass spectrometry, and metabolomics using HPLC-diode array detector-MS (HPLC-DAD-MS), partial least squares regression analysis (PLS-DA), and a correlation map (univariate correlation analyses) enabled the prediction of compounds that have a positive
Enantioenriched α-substituted glutamates/pyroglutamates via enantioselective cyclopropenimine-catalyzed Michael addition of amino ester imines
Beilstein J. Org. Chem. 2021, 17, 2077–2084, doi:10.3762/bjoc.17.134
- organizational interactions. This complexity makes the detailed prediction of the transition state organization for the current process very challenging. However, we propose that the general structure 19 shown in Figure 3 is a reasonable representation of one of the likely pathways (the major ambiguities being
A study on selective transformation of norbornadiene into fluorinated cyclopentane-fused isoxazolines
Beilstein J. Org. Chem. 2021, 17, 2051–2066, doi:10.3762/bjoc.17.132
- the structure of a certain metathesis substrate, the nature of the catalyst and all experimental conditions may highly influence metathesis reactions and determine the outcome of olefin metathesis. The accurate prediction of a specific catalyst, including its efficiency, the suitable experimental
- outcome of metathesis, various publications were dedicated to studies describing selective CM or ROCM transformations. The accurate prediction of selectivity regarding CM reactions is still considered to be a challenging issue among synthetic organic chemists. Of numerous factors contributing to the
- general model suitable for the prediction of product selectivity and olefin bond chemodifferentiation in cross metathesis. In general, regarding the reactivity of the olefin bond in CM, alkenes can be categorized by the relative ability to undergo homodimerization via CM and the possibility of the
Electron-rich triarylphosphines as nucleophilic catalysts for oxa-Michael reactions
Beilstein J. Org. Chem. 2021, 17, 1689–1697, doi:10.3762/bjoc.17.117
- acceptors, Michael donors and catalysts used in this study; pKa (respectively pKa of the conjugated acid in case of phosphines) calculated using the pKa prediction platform (neural network result for solvent H2O) available at pka.luo-group.com [20]; below: Conversion of the oxa-Michael reaction of
Methodologies for the synthesis of quaternary carbon centers via hydroalkylation of unactivated olefins: twenty years of advances
Beilstein J. Org. Chem. 2021, 17, 1565–1590, doi:10.3762/bjoc.17.112
- patterns and electronic features were measured previously by the rate of deuterium/hydrogen exchange [77], and the observed constants served as a guide to the regioselectivity prediction of the HAT processes in substrates with different olefins. In substrate 40, for example, the hydrogen atom was
N-tert-Butanesulfinyl imines in the asymmetric synthesis of nitrogen-containing heterocycles
Beilstein J. Org. Chem. 2021, 17, 1096–1140, doi:10.3762/bjoc.17.86
Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams
Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12
- new, chiral 2-(tetrazol-5-yl)-iminosugar based potential organocatalyst. Principle behind Woerpel’s model for prediction of the direction of nucleophile addition to oxocarbenium cations. Difference in conformational stability of glucose- and galactose-derived iminium cations and the major product of
Molecular basis for protein–protein interactions
Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1
- functionality and the corresponding pathways. Important roles of PPIs include hormone reception [2], protease inhibition [3], antibody–antigen complexes [4], gene regulation [5], and large biomolecular assemblies [6]. PPI identification and prediction are important for targeting anticancer strategies [7
Dawn of a new era in industrial photochemistry: the scale-up of micro- and mesostructured photoreactors
Beilstein J. Org. Chem. 2020, 16, 2484–2504, doi:10.3762/bjoc.16.202
- , an empirical formula was suggested for the prediction of the optical path length in gas–liquid flows [75]. The photon transport, together with the hydrodynamics in the commercially available Corning G1 Advanced-FlowTM reactor (G1 AFR) was studied. A Corning AFR was shown in the previous section in
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
- preferences. It is worth mentioning that Igg has two gauche relationships between C–F and C–O bonds, which is stabilized by σCH → σCF/CO hyperconjugative interactions [14]. Second, we have searched for the implications of the relative conformational stabilities for log P prediction, the most common parameter
- module of the ACD/Labs program) yields a similar result (r2 = 0.71, see Figure S1 in Supporting Information File 1). Moreover, from Figure 5b, due to the high slope and the resulting intercept, one can assume the existence of a systematic error associated with the prediction of log P. This finding
- reinsures the issues with additive methods for predicting lipophilicity of complex structures as those analyzed herein. Nevertheless, a reservation should be considered for small organofluorine compounds, for which well-parameterized models for log P prediction are usually available. Regarding the use of
Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups
Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182
- clearly indicates that further research towards theoretical lipophilicity prediction based in relative Gibbs energies in water and (wet) octanol is required. Examples of lipophilicity modulation for geminal dimethyl to cyclopropyl and oxetane modifications (measured experimentally via shake-flask method
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
- monosaccharides. We define these “glycoblocks” as self-contained 3D units, uniquely identified by the nature of the residues they comprise, their linkages and structural/dynamic features. This alternative description of glycans’ 3D architecture can potentially lead to an easier prediction of sequence-to-structure
Design, synthesis and application of carbazole macrocycles in anion sensors
Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157
- different solvent systems to select three champions for constructing anion sensor prototypes. Binding studies in solution suggested selectivity towards acetate, however, this prediction did not hold true once the ionophores were incorporated into sensors. Overall, the constructed sensor prototypes showed
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