Center for Functional Nanomaterials Seminar

Abstract:
FFT based sampling approaches enable effective search of mutual orientations of two rigid body atom configurations. Despite rigidity limitation, this approach proved to be very effective for modeling a large class of protein-protein interactions, as well as special cases of protein ligand interactions. My talk consist of three parts. In the first part I will demonstrate that the approximation is accurate enough not just to model the structure of the complex, but also provides insight in protein-protein association, and reveals insight about the protein interaction energy landscape. Currently FFT sampling acceleration is currently achieved only on a 3D subspace of the full 6D rotational/translational space, and the remaining dimensions must be sampled using conventional slow calculations. In the second part I will present an algorithm that employs FFT-based sampling on the 5D rotational space, and only the 1D translations are sampled conventionally. The accuracy of the results is the same as those of earlier methods, but the calculation is an order of magnitude faster. Also, it is inexpensive computationally to add more correlation function terms to the scoring function compared with classical approaches. Finally in the third part of the talk I will discuss the strategies to expand the approach for flexible sampling.