Simulations for benchmarking interactive flexible molecular docking for Virtual Reality in DockIT

This series of flexible-receptor docking simulations were developed to benchmark interactive docking performance in DockIT. There are seven test cases comprising a varying range of atoms up to approximately 92,000. The seven pairs are detailed below. Molecule Pair (Receptor-Ligand) Receptor created from MD Simulation Number of Atoms in Receptor Number of Atoms in Ligand GGG–GLTM Yes 3431 20 HDAC–OJ Yes 5478 41 OMP–MLTS Yes 5737 45 2X_OMP–2X_OMP Created from OMP 11474 11474 4X_OMP–4X_OMP Created from 2X_OMP 22948 22948 8X_OMP–8X_OMP Created from 4X_OMP 45896 45896 16X_OMP–16X_OMP Created from 8X_OMP 91792 91792 The first three pairs for benchmarking are molecular structure files downloaded from the PDB. Molecular Dynamics Simulations are performed on the receptors to obtain a molecular dynamics trajectory. The trajectories and original PDB files are used to compute the eigen vectors and eigen values following the approach as detailed here: https://colab.research.google.com/drive/1i7db2LINovZGhvQJmls9oOqpfYnOofKf?usp=sharing Further details on the simulations for Maltose Binding Protein (OMP above) and Glutamine Binding Protein (GGG above) can be found here https://doi.org/10.1021/acs.jcim.9b00112. For HDAC please refer to https://pubs.acs.org/doi/10.1021/acs.jchemed.4c01347. For the purposes of benchmarking larger structures, the OMP structure from above is extended by copying the information created for OMP. We constructed 2X_OMP and 8X_OMP by stacking respectively OMP and 4X_OMP molecules along their first principal axis. Whereas we constructed 4X_OMP and 16X_OMP by stacking respectively 2X_OMP and 8X_OMP molecules along their second principal axis.