Projects

Our main aim is to develop and apply computer-aided methods to model, simulate and predict how biomolecules interact. The focus is on the interactions of proteins. The methods make use of three-dimensional macromolecular structures and combine approaches based on physicochemical principles with those of chemo- and bio-informatics.
Some of our projects are described on this page.

Structure-based drug discovery

Proteins are dynamic and constantly changing their shape. This flexibility not only presents a challenge to to structure-based drug design approaches but also opportunities for the design of specific compounds with suitable kinetic properties. We are developing methods to model and simulate protein and ligand dynamics in order to identify transient binding pockets in proteins…

Macromolecular interactions and diffusional association

We are developing methods to predict protein-protein interactions and how proteins bind to surfaces. These methods rely on Brownian dynamics simulation with SDA and molecular dynamics simulation. In SDA can be used to simulate the association of two solutes, e.g. two proteins, in implicit solvent. SDA can also be applied to simulate the diffusion of…

Protein structures in systems biology

We are working on developing approaches to bridge between protein structures and biochemical networks, from the molecular to the cellular level. We have recently released LigDig, a webserver for querying ligand-protein interactions. It has been designed to assist users in systems biology projects with queries that require access to multiple data sources as well as…