Current Medicinal Chemistry - Volume 27, Issue 38, 2020

Background: The KNIME platform offers several tools for the analysis of chem- and pharmacoinformatics data. Unless one has sufficient in-house data available for the analysis of interest, it is necessary to fetch third party data into KNIME. Many data sources offer valuable data, but including this data in a workflow is not always straightforward. Objective: Here we discuss different ways of accessing public data sources. We giv Read More

In recent years there has been a paradigm shift in how data is being used to progress early drug discovery campaigns from hit identification to candidate selection. Significant developments in data mining methods and the accessibility of tools for research scientists have been instrumental in reducing drug discovery timelines and in increasing the likelihood of a chemical entity achieving drug development milestones. KNIME Read More

Drug discovery is a challenging and expensive field. Hence, novel in silico tools have been developed in early discovery stage to identify and prioritize novel molecules with suitable physicochemical properties. In many in silico drug design projects, molecular databases are screened by virtual screening tools to search for potential bioactive molecules. The preparation of the molecules is therefore a key step in the succes Read More

Since the official release as a KNIME Community Contribution in June 2013, the Vernalis KNIME nodes have increased from a single node (the ‘PDB Connector’ node) to around 126 nodes (November 2017; Version 1.12.0); furthermore, a number of nodes have been adopted into the core KNIME product. In this review, we provide a brief timeline of the development of the current public release and an overview of the current nod Read More

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we Read More

A number of clinical studies have revealed that there is an association between major depression (MD) and gastroesophageal reflux disease (GERD). Both the diseases are shown to affect a large proportion of the global population. More advanced studies for understanding the comorbidity mechanism of these two diseases can shed light on developing new therapies of both diseases. To the best of our knowledg Read More

Background: Gangliosides are an essential component of eukaryotic plasma membranes implicated in multiple physiological processes. Little is known about molecular mechanisms underlying the distribution and functions of membrane gangliosides. The overwhelmingly complex organization of glycocalyx impedes the structural analysis on cell surface and the interplay between the lipid components. Advanced X-r Read More