Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

Chemical structure generators are used in cheminformatics to produce or enumerate virtual molecules based on a set of boundary conditions. The result can then be tested for properties of interest, such as adherence to measured data or for their suitability as drugs. The starting point can be a potentially fuzzy set of fragments or a molecular formula. In the latter case, the generator produces the set of constitutional isomers of the given input formula. Here we present the novel constitutional isomer generator based on the canonical generation path method. uses the package to compute automorphism groups of graphs. We outline the working principles of and present benchmarking results which show that is currently the fastest structure generator. is available under a liberal open-source license.

Chemical graph generators are software packages to generate computer representations ofchemical structuresadhering to certainboundary conditions. Their development is a research topic ofcheminformatics. Chemical graph generators are used in areas such as virtuallibrarygeneration indrug design, inmolecular designwith specified properties, called inverseQSAR/QSPR, as well as inorganic synthesis design,retrosynthesisor in systems forcomputer-assisted structure elucidation(CASE). CASE systems again have regained interest for the structure elucidation of unknowns in computationalmetabolomics, a current area ofcomputational biology.

Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries for their high bioactivities. Over the years a multiplication of thematic NP databases has been observed. However, there is no online resource regrouping all known NPs in just one place, which would greatly simplify NP research and allow computational screening and other in silico applications. Here we present the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of NPs available in different open sources and a subsequent web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering. Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.

Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the literature, there are various types of reservoirs ranging from in-silico to in-vitro. In cheminformatics, previous studies contributed to the field by developing simulation-based chemically inspired in-silico reservoir models. Yahiro used a DNA-based chemical reaction network as its reservoir and Nguyen developed a DNA chemistry-inspired tool based on Gillespie algorithm. However, these software tools were designed mainly with the focus on DNAchemistry and their maintenance status has limited their current usability. Due to these limitations, there was a need for a proper open-source tool. This study introduces ChemReservoir, an open-source framework for chemically-inspired reservoir computing. In contrast to the former studies focused on DNA-chemistry, ChemReservoir is a general framework for the construction and analysis of chemically-inspired reservoirs, which also addresses the limitations in these previous studies by ensuring enhanced testing, evaluation, and reproducibility. The tool was evaluated using various cycle-based reservoir topologies and demonstrated stable performance across a range of configurations in memory capacity tasks.