This repository contains the source codes and data needed to replicate our research on USP7 interactions with its substrate Ubiquitin-Rhodamine-110-Gly
- The folder "1_Generation_of_the_models" contains the setup files used for modelling the enzyme-substrate complexes between USP7 and the substrate Ub-Rho in its variants RHA and RHB. The ΔCTL models were generated by deleting the CTL's residues from 1083 to 1102 from the respective FS models.
- The folder "2_MD_simulations" contains: 1) The subfolder "2.1_Preparation_of_the_MD_input_files" with the scripts for generating using tleap (the run.inp files) the amber topology (parm7 files) and coordinates (rst7 files) for the MD simulations. We also provided the prepi and frcmod files generated using antechamber and the models of the enzyme-substrate complexes (in pdb format) generated using modeller and refined using the protein preparation wizard protocol through Maestro interface. 2) The subfolder "2.2_MD_simulations_setup" with the bash scripts and the input files for running our MD simulation protocol using pmemd. 3) The subfolder "2.3_MD_simulations_outputs_and_analyses" with: the output files from the productive MD simulations using pmemd (in "Productive_MD_outputs_by_replica"); the CPPTraj scripts for performing the RMSF analysis (in "RMSF"); and the CPPTraj scripts and some of the outputs from the PCA analysis (in "PCA+cluster_centroids").
- The folder "3_MMGBSA" contains the scripts and the input files uses for performing the MMGBSA analysis. Here, we also included the pdb and topology files for the enzyme ("_MMPBSA_receptor.pdb" and "RECEPTOR.parm7"), the substrate ("_MMPBSA_ligand.pdb" and "LIGAND.parm7") and the complex ("_MMPBSA_COMPLEX.pdb" and "COMPLEX.parm7") generated during the analysis.