MD simulation input and trajectory files of protac ternary complexes.

Input and trajectory files for MD simulation of 5 test cases for article titled "Shotgun Approach for PROTAC Ternary Complex Modeling and Evaluation". Only ternary complexes were extracted from the MD trajectories to save space. All the input files needed for SPONGE run were uploaded. For 5 test systems: "XXXX_SPONGE_input.zip" contains the input files for SPONGE run. "XXXX_runx_min_MD.pdb" is the trajectory from minimization. "XXXX_runx_MD_traj_centered.zip" contains the trajectory from 100ns NPT run. For the 10 clusters of ternary complexes generated for 8QJR: "8QJR_DSDP_clusterx_SPONGE_input.zip" contains the input files for SPONGE run. "8QJR_DSDP_clusterx_min_MD.pdb" is the trajectory from minimization. "8QJR_DSDP_clusterx_MD_traj_centered.zip" contains the trajectory from 100ns NPT run.