Docking Paradigm in Drug Design.

Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described.

Supercomputer docking with a large number of degrees of freedom.

Docking represents one of the most popular computational approaches in drug design. It has reached popularity owing to capability of identifying correct conformations of a ligand within an active site of the target-protein and of estimating the binding affinity of a ligand that is immensely helpful in prediction of compound activity. Despite many success stories, there are challenges, in particular, handling with a large number of degrees of freedom in solving the docking problem.

Steady oscillations in aggregation-fragmentation processes.

We report surprising steady oscillations in aggregation-fragmentation processes. Oscillating solutions are observed for the class of aggregation kernels K_{i,j}=i^{ν}j^{μ}+j^{ν}i^{μ} homogeneous in masses i and j of merging clusters and fragmentation kernels, F_{ij}=λK_{ij}, with parameter λ quantifying the intensity of the disruptive impacts. We assume a complete decomposition (shattering) of colliding partners into monomers.

Oscillations in Aggregation-Shattering Processes.

We observe never-ending oscillations in systems undergoing collision-controlled aggregation and shattering. Specifically, we investigate aggregation-shattering processes with aggregation kernels K_{i,j}=(i/j)^{a}+(j/i)^{a} and shattering kernels F_{i,j}=λK_{i,j}, where i and j are cluster sizes, and parameter λ quantifies the strength of shattering. When 0≤a<1/2, there are no oscillations, and the system monotonically approaches a steady state for all values of λ; in this region, we obtain an analytical solution for the stationary cluster size distribution.

Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms.

We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum.