Multiscale simulations

Structural flexibility of biomolecules is closely coupled to function, as evidenced by many conformational changes observed on key cellular process. We actively work to effectively address the study and simulation of the dynamics of biomolecular systems with Normal-Mode Analysis (NMA), geometric algebra and other multiscale approximations.

Following the basic principle if you know how it moves, you can infer how it works; the knowledge of structural flexibility offers a straight-line connection between structure and function. Thus, inferring the intrinsic molecular flexibility from a single conformation could offer a direct link to understand likely large scale rearrangements. We are adressing this problem by exploring novel multiresolution approaches to simulate the dynamics of protein, RNA and their complexes. For example, iMOD is an versatile toolkit to perform Normal Mode Analysis (NMA) in internal coordinates on both protein and nucleic acid atomic structures. DFprot is a web-based server for predicting main-chain deformability from a single protein conformation. The server automatically performs a NMA (Cartesian) of the uploaded structure and calculates its capability to deform at each of its residues.