TU Dresden
A joint project with Uni Leipzig DE EN

Spinnaker Cloud Computing for Computer-aided Drug Discovery

Mentored by Jens Meiler, Christian Mayr
at Institute for Drug Disocvery, Medical School, Leipzig University

Virtual high throughput screening (vHTS) is an essential tool in drug discovery to select molecules for experimental testing as the space of drug-like molecules (up to 1060) is far too large for experimental screening. vHTS techniques in academia and start-up companies experience a revolution as three developments coincide: a) new companies provide large (1010) make-on-demand chemical libraries where compounds that emerge from vHTS can be ordered economically; b) innovative artificial intelligence (AI) methods developed by us and others improve vHTS results by providing better quantitative structure-activity relationship (QSAR) models; and c) deep learning protein structure prediction methods such as AlphaFold and RoseTTAFold are adapted by us and others to create protein structures suitable for vHTS.

Here we propose to combine these innovative technologies pioneered in the Meiler laboratory at Leipzig University within SECAI with an innovative hardware setup also built within SECAI, the newly developed Spinnaker2 at TU Dresden. It provides up to ten million computational cores. We hypothesize that Spinnaker2 can be programmed to meet the computational demands of vHTS and thus allow the screening of complete make-on-demand compound libraries for the first time.

Work Environment

You will be working with both PIs to implement drug discovery algorithms on Spinnaker2. Your algorithms will be used for drug discovery. Molecules will be synthesized and tested for biological activity on a number of application projects. Current application projects include drug development for neurological diseases including Schizophrenia, Alzheimer's, and Parkinson’s, probing the fundamentals of G-protein-coupled receptor signaling, understanding cardiac arrhythmia as caused by the complex interplay of potassium channel regulation and drug interactions, multidrug resistance in cancer and bacterial cells related to multidrug transporter proteins, and the structural basis of viral infections and antibody activity, among others.

Prerequisites

To conduct this research, you should hold a very good university degree (MSc or an equivalent) in computer science, chemistry, bioinformatics or related disciplines.