Calculation of binding free energy between interacting proteins

The calculation results of data and scripts can refer to the article published in the Chinese Journal of Bioengineering: "Application of Bioinformatics in Analysis, Modification, and De novo Design of Interacting Proteins" DOI: 10.13523/j.cb.202502014. 1. The 22 interacting protein structure files in. pdb format in the PDBs folder are from the PDB database（ rcsb.org/ ）The downloaded material is divided into dimer structure (A_B folder) and trimer structure (A_HL folder). 2.

The 'data. xlsx' table file records data from PDBbind（ pdbbind-plus.org.cn/ ）The binding affinity data obtained from the experiments of these 22 interacting proteins, as well as the binding free energy data calculated using four tools: Rosetta, PyRosetta, GROMACS, and PRODIGY. 3. The scripts folder contains the calculation scripts for Rosetta, PyRosetta, and GROMACS, as well as instructions on how to use these scripts, including the source and instructions for using them. txt.