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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 graph generators are software packages to generate computer representations of chemical structures adhering to certain boundary conditions . Their development is a research topic of cheminformatics . Chemical graph generators are used in areas such as virtual library generation in drug design , in molecular design with specified properties, called inverse QSAR/QSPR , as well as in organic synthesis design , retrosynthesis or in systems for computer-assisted structure elucidation (CASE). CASE systems again have regained interest for the structure elucidation of unknowns in computational metabolomics , a current area of computational biology .

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 surge based on the canonical generation path method. Surge uses the nauty package to compute automorphism groups of graphs. We outline the working principles of surge and present benchmarking results which show that surge is currently the fastest structure generator. Surge is available under a liberal open-source license.

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 in single-threaded mode against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution PMG. Based on the benchmarking, MAYGEN is on average 47 times faster than PMG and on average three times slower than MOLGEN in performance.

We present a general framework to generate trees every vertex of which has a non-negative weight and a color. The colors are used to impose certain restrictions on the weight and colors of other vertices. We first extend the enumeration algorithms of unweighted trees given in [19, 20] to generate weighted trees that allow zero weight. We avoid isomorphisms by generalizing the concept of centroids to weighted trees and then using the so-called centroid-rooted canonical weighted trees. We provide a time complexity analysis of unranking algorithms and also show that the output delay complexity of enumeration is linear. The framework can be used to generate graph classes taking advantage of their tree-based decompositions/representations. We demonstrate our framework by generating weighted block trees which are in one-to-one correspondence with connected block graphs. All connected block graphs up to 19 vertices are publicly available at [1].

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.