Web tool for graph embeddings representation techniques evaluation

Author(s):  
I. Ivanoska ◽  
M. Milenkoski ◽  
S. Kalajdziski ◽  
K. Trivodaliev
2019 ◽  
Author(s):  
Devendra K. Dhaked ◽  
Wolf Ihlenfeldt ◽  
Hitesh Patel ◽  
Marc Nicklaus

<p>We have collected 86 different transforms of tautomeric interconversions. Out of those, 54 are for prototropic (non-ring-chain) tautomerism; 21 for ring-chain tautomerism; and 11 for valence tautomerism. The majority of these rules have been extracted from experimental literature. Twenty rules – covering the most well-known types of tautomerism such as keto-enol tautomerism – were taken from the default handling of tautomerism by the chemoinformatics toolkit CACTVS. The rules were analyzed against nine differerent databases totaling over 400 million (non-unique) structures as to their occurrence rates, mutual overlap in coverage, and recapitulation of the rules’ enumerated tautomer sets by InChI V.1.05, both in InChI’s Standard and a Non-Standard version with the increased tautomer-handling options 15T and KET turned on. These results and the background of this study are discussed in the context of the IUPAC InChI Project tasked with the redesign of handling of tautomerism for an InChI version 2. Applying the rules presented in this paper would approximately triple the number of compounds in typical small-molecule databases that would be affected by tautomeric interconversion by InChI V2. A web tool has been created to test these rules at https://cactus.nci.nih.gov/tautomerizer.</p>


2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Noé Cécillon ◽  
Vincent Labatut ◽  
Richard Dufour ◽  
Georges Linarès

2019 ◽  
Vol 31 (1) ◽  
Author(s):  
Kees J. M. Kramer ◽  
Frank Sleeuwaert ◽  
Guy Engelen ◽  
Christin Müller ◽  
Werner Brack ◽  
...  

Abstract Chemical pollution of water bodies is a complex problem around the globe. When described by the extremes of the range of problem definitions, water bodies can be chemically polluted by a single compound that is emitted from a point source or an incidental spill, or by chronic diffuse emissions from local and upstream land uses. The resulting mixture exposures can vary in space and time, e.g. due to the use of pesticides in the crop growing season. The environmental management objectives are commonly to protect and restore surface waters against human influences. Currently, chemical pollution is globally judged for a selected set of compounds, by judging each of these individually in comparison with protective environmental quality standards. Research has provided a novel assessment paradigm (solution-focused risk assessment) and novel data, measurement methods and models to improve on current practices. Their adoption and application require establishing novel linkages between the diverse problem definitions and the novel approaches. That would assist water quality professionals to select the most effective option or options to protect and restore water quality. The present paper introduces the RiBaTox (River Basin Specific Toxicants assessment and management) web tool. It consists of short descriptions of the novel approaches (made available as Additional file 1) and a decision tree for end-users to select those. The overview of novel approaches collated in RiBaTox is relevant for end-users ranging from local water quality experts up till strategic policy developers. Although RiBaTox was developed in the context of European water quality problems, the methods provided by RiBaTox are relevant for users from (inter)national to local scales. This paper is part of a series of Policy Briefs from the EU-FP7 project SOLUTIONS (http://www.solutions-project.eu), which provide backgrounds on chemical pollution of surface waters and policy practices and proposed improvements.


Author(s):  
Defu Yang ◽  
Jiazhou Chen ◽  
Chenggang Yan ◽  
Minjeong Kim ◽  
Paul J. Laurienti ◽  
...  

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