Medicinal Chemists AIMMS develop Virtual Machine for Computer-Aided Drug Discovery
A team of cheminformatics and bioinformatics researchers from AIMMS (VU Amsterdam), Radboudumc Nijmegen, BioAxis Research, and Netherlands eScience Center have developed a freely available virtual machine to enable computer-aided drug design.
The 3D-e-Chem consortium, including Marton Vass, Albert Kooistra, and Chris de Graaf (PI) from the Medicinal Chemistry research group, develop new cheminformatics technologies to improve the integration of chemical and biological data for the prediction of structural interactions between drug molecules and therapeutic protein targets. The computational drug discovery platform is currently applied to identify and optimize molecules that act on several proteins simultaneously (polypharmacology), while avoiding undesired side effects via interactions with off-target proteins.
The 3D-e-Chem software tools and virtual machine (see figure) are described in a recent publication in the Journal of Chemical Modeling and Information and the computational building blocks (nodes) that enable researchers to design their own drug discovery workflows have been incorporated in KNIME, the leading open data analytics platform.