Ben
Ries

Agile development of an open-source package for free energy calculations to predict molecule potency in an international team of six developers

Development of combined physical modeling and machine learning solutions for medicinal chemistry R&D efforts. Testing and evaluation of state-of-the-art commercial software for project implementation purposes. Supervision of a master student project. Introduction to drug discovery research workflows.

Method development and collaboration with experimental scientists with in silico rationalization in cyclic-peptide design. Planning and supervision of student projects/theses, teaching lecture seminars. Presenting work to professional audiences at international conferences.

Studying a protein-ligand complex with docking methods and molecular dynamics simulations, analysis of protein homology on a sequence level.

Biosynthesis of peptides, interaction studies with 2D-NMR, cloning, bacterial cell culture, protein purification.

Free Energy Methods: Drug-Like Molecules and Macrocycles

(Prof. Dr. Sereina Riniker) Enhancements of the free energy calculation method RE-EDS for drug design. In silico studies on membrane permeability of macrocycles.

Extra-Curricular Coursework:

Microeconomics, Macroeconomics, Human Resource Management: Leading Teams, Agile Project Management, Software Design

Drug Design, Massively Parallel Computing, Visualization of Biological Data, Structural Biology

Thesis:

Modelling Dinoflagellate luciferase-luciferin complex with constant pH MD (Prof. Dr. David van der Spoel, Prof. Dr. Oliver Kohlbacher).

Structural Biology, Organic Biochemistry, Cell Biochemistry, Applied Bioinformatics.

Thesis:

Structural studies of cell polarity proteins in context of metastasis induction (Dr. Silke Wiesner, MPI for Biology Tübingen ).

Biology, History and Informatics