Modeling of structure, folding and interactions of biomolecules in the era of GPGPU computing

The recent boom in general-purpose computing on graphics processing units (GPGPU) facilitates simulations with high demands on computer resources. Such simulations are typical for macromolecules and nanoparticles of biological importance. Several proteins, instead of folding into biologically active 3D structures, aggregate together forming large fibril structures called amyloid aggregates. Amyloids are being extensively studied both experimentally and through computer simulations. Since amyloid aggregates are huge molecular complexes composed from hundreds of thousands of atoms, it is clear that their simulations need supercomputing power. GPGPU-based clusters were shown to offer alternative resources for performing molecular dynamics simulations on nanoscale. We were also using one of the newest docking methodology (the AutoDock Vina program) to model the differences in ligand binding to the native insulin and to the unfolded complexes. In addition, virtual lectin arrays were constructed and high-throughput “In Silico” screening was performed in order to select the best binders to the particular galectins.