Hybrid methods

Hybrid methods

Bridging the resolution gap with hybrid methods
Protein modeling

Protein modeling

Modeling protein structures and their interactions
Multiscale dynamics

Multiscale dynamics

Exploring the macromolecular biomachines dynamics
Drug Discovery

Drug Discovery

Computer-aided rational drug design and discovery

Protein Modeling

We develop tools for modeling protein structures and their interactions. This includes novel methods for:

  • Protein-protein docking. Predict how two or more proteins can interact from its individual unbound components can reveal new insights in the basic principles of molecular recognition. Moreover, the better understanding of protein-protein interactions can be useful for structure-based drug design and other applications. Our research interests include the development of tools to address this otherwise high demanding computational problem.  Please have a look to our FRODOCK server for the prediction of protein-protein interactions using an improved version of our Fast Rotational DOCKing method. Given the 3D coordinates of two interacting proteins the server generates very efficiently many potential predictions of how they could interact. 
  • Loop modeling. RCD+ server is a fast and accurate loop-closure modeling tool.  Accurate all-atom loop predictions and ensembles can be easily generated in only few minutes.
  • Coarse-gained potential. Our Knowledge-base ORientational Potential  (KORP) utilizes a 6D joint probability and a minimalist representation to outperform state-of-the-art statistical potentials for protein and loop modeling. Our side-chain independent potential is a fast and highly discriminating energy function, please have a try.