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.

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.