In this paper, we compare the most popular Atom-to-Atom Mapping (AAM) tools: ChemAxon, [1] Indigo, [2] RDTool, [3] NameRXN (NextMove), [4] and RXNMapper [5] which implement different AAM algorithms. An open-source RDTool program was optimized, and its modified version ("new RDTool") was considered together with several consensus mapping strategies. The Condensed Graph of Reaction approach was used to calculate chemical distances and develop the "AAM fixer" algorithm for an automatized correction of erroneous mapping. The benchmarking calculations were performed on a Golden dataset containing 1851 manually mapped and curated reactions. The best performing RXNMapper program together with the AMM Fixer was applied to map the USPTO database. The Golden dataset, mapped USPTO and optimized RDTool are available in the GitHub repository https://github.com/Laboratoire-de-Chemoinformatique.

Finding synthesis routes for molecules of interest is essential in the discovery of new drugs and materials. To find such routes, computer-assisted synthesis planning (CASP) methods are employed, which rely on a single-step model of chemical reactivity. In this study, we introduce a template-based single-step retrosynthesis model based on Modern Hopfield Networks, which learn an encoding of both molecules and reaction templates in order to predict the relevance of templates for a given molecule. The template representation allows generalization across different reactions and significantly improves the performance of template relevance prediction, especially for templates with few or zero training examples. With inference speed up to orders of magnitude faster than baseline methods, we improve or match the state-of-the-art performance for top- k exact match accuracy for k ≥ 3 in the retrosynthesis benchmark USPTO-50k. Code to reproduce the results is available at .

The quality of experimental data for chemical reactions is a critical consideration for any reaction-driven study. However, the curation of reaction data has not been extensively discussed in the literature so far. Here, we suggest a 4 steps protocol that includes the curation of individual structures (reactants and products), chemical transformations, reaction conditions and endpoints. Its implementation in Python3 using CGRTools toolkit has been used to clean three popular reaction databases Reaxys, USPTO and Pistachio. The curated USPTO database is available in the GitHub repository (Laboratoire-de-Chemoinformatique/Reaction_Data_Cleaning).

The stereoselective preparation of a novel 4’-spirocyclopropyl nucleoside analogue has been described using a semi-benzilic Favorskii rearrangement of a 4’-(2-chloro-3-oxocyclobutyl)spirofuranose as a key step. We demonstrated that the latter chiral spirocyclic intermediates, readily obtained on multigram scale from chiral pool starting materials, are highly suitable precursors to obtain full stereoselectivity in the reduction-ring contraction sequence. The downstream nucleobase introduction via Vorbrüggen glycosylation successfully resulted in the formation of the corresponding novel 4’-spirocyclic nucleoside analogue in a stereospecific manner.

Signal-to-noise-ratio (SNR) images were constructed by a sliding window technique. Theoretical derivations of the first order statistical properties of SNR images are given for the case of intensity coding of the original images for low number densities and for the limit case of fully developed speckle. The original images were obtained by realistic simulations of backscattering by homogeneous media, while using a range of number densities of the scatterers (isotropic scattering). The SNR imaging method is illustrated by results obtained from simulated scattering media containing a lesion that is contrasting in reflectivity level or in number density of the scatterers. A considerable improvement in lesion detection is obtained if the primary difference from the background speckle is due to a different number density of the scatterers within the lesion.

Cyclopropane fusion of the only rotatable carbon–carbon bond in furanosyl nucleosides (i.e., exocyclic 4′–5′) is a powerful design strategy to arrive at conformationally constrained analogues. Herein, we report a direct stereodivergent route toward the synthesis of the four possible configurations of 4-spirocyclopropane furanoses, which have been transformed into the corresponding 4′-spirocyclic adenosine analogues. The latter showed differential inhibition of the protein methyltransferase PRMT5-MEP50 complex, with one analogue inhibiting more effectively than adenosine itself, demonstrating the utility of rationally probing 4′–5′ side chain orientations.

An objective measure (Lesion Signal-to-Noise Ratio) quantifying the detectability of lesions in echographic images was employed. This measure was used to determine the performance of digital speckle reduction filters, which were applied to computer simulated ultrasound B-mode images. One linear (mean filter) and two nonlinear filters (median and L2-mean filters) have been investigated. A comparison was made between fixed and adaptive versions of these filters. The influence of the size of the filter window on the Lesion Signal-to-Noise Ratio was systematically investigated. Also, the effect of the shape of the filter window is illustrated. The difference in performance of the linear and nonlinear filters was found to be small. Adaptive filters did not perform significantly better than fixed filters. The maximum improvement of lesion detectability was in the order of 40 percent. The choice of a correct window size was critical. For all types of filters, an optimum window size appeared to be present in the curves relating the Lesion Signal-to-Noise Ratio to this size.

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