Publication: Medicinal chemistry in the era of big data

In the era of big data medicinal chemists are exposed to an enormous amount of bioactivity data. Numerous public data sources allow for querying across medium to large data sets mostly compiled from literature. However, the data available are still quite incomplete and of mixed quality. This mini review will focus on how medicinal chemists Read more about Publication: Medicinal chemistry in the era of big data[…]

Publication: Transporter taxonomy – a comparison of different transport protein classification schemes

Currently, there are more than 800 well characterized human membrane transport proteins (including channels and transporters) and there are estimates that about 10% (approx. 2000) of all human genes are related to transport. Membrane transport proteins are of interest as potential drug targets, for drug delivery, and as a cause of side effects and drug–drug Read more about Publication: Transporter taxonomy – a comparison of different transport protein classification schemes[…]

Publication: Transporter assays and assay ontologies: useful tools for drug discovery

Transport proteins represent an eminent class of drug targets and ADMET (absorption, distribution, metabolism, excretion, toxicity) associated genes. There exists a large number of distinct activity assays for transport proteins, depending on not only the measurement needed (e.g. transport activity, strength of ligand–protein interaction), but also due to heterogeneous assay setups used by different research Read more about Publication: Transporter assays and assay ontologies: useful tools for drug discovery[…]

Publication: Scientific competency questions as the basis for semantically enriched open pharmacological space development

Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of an open pharmacological space (OPS) Read more about Publication: Scientific competency questions as the basis for semantically enriched open pharmacological space development[…]

Publication: Open PHACTS: Semantic interoperability for drug discovery

Open PHACTS is a public–private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an ‘open pharmacological space’ using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve specific questions in drug discovery Read more about Publication: Open PHACTS: Semantic interoperability for drug discovery[…]

Publication: Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation

In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to ensure that the data are high Read more about Publication: Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation[…]

Publication: Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research

Systems chemical biology, the integration of chemistry, biology and computation to generate understanding about the way small molecules affect biological systems as a whole, as well as related fields such as chemogenomics, are central to emerging new paradigms of drug discovery such as drug repurposing and personalized medicine. Recent Semantic Web technologies such as RDF Read more about Publication: Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research[…]