What do we do?
At the Computational Structural Biology (CSB) Group we are focusing on the development of methods and algorithms to model, simulate and analyse three-dimensional protein structures and their molecular properties in order to apply these techniques to understanding biological processes at a molecular level. Our main emphasis is on homology modelling approaches – using evolutionary information to model protein tertiary and quaternary structures. Applications in biomedical research include the study of protein-ligand interactions from different perspectives, such as the identification of small antiviral molecules to support drug development, the structure-guided engineering of enzymes or the interpretation of disease causing mutations in proteins.
In a collaboration with the Swiss Federal Laboratories for Materials Science and Technology, and GlycoVaxyn AG (Schlieren, Switzerland), our group successfully engineered the specificity of a recombinant bacterial enzyme for the production of novel conjugate vaccines in E.coli. Computational modelling of the protein structure in complex with potential substrates provided the basis for the rational engineering of the enzyme’s properties.
In June, the group organized the 12th edition of the Basel Computational Biology Conference: The meeting brought together over 500 scientists from a broad range of disciplines. The next [BC]2 Conference is planned for September 2017.
In November, our team presented a novel user interface experience for exploring molecular interactions at the Swiss Innovation Forum in Basel – the national platform for promoting innovation, creativity and design. Transforming the molecular forces resulting from such simulations into a physical force, which can be perceived using a haptic feedback device, provides a new and innovative user interface experience.
Main publications 2015
- Kryshtafovych A et al. Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11. Proteins 2015;doi:10.1002/prot.24919.
- Sali A et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure: with folding and design 2015;23(7):1156-67.
- Ihssen J et al. Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering. Open Biol 2015;5(4):140227.