BindingSiteSolvation

This repository provides input files and results for the study of Solvation Thermodynamic Costs of Cognate Binding Site Formation. The content is organized into the following folders:

Data

This folder contains:

• GIST integration results
• SSTMap hydration site analysis results of 34 DUD-E systems.

MD_Input_files

This folder contains:

• MD input files for both rigid and flexible simulations.

• .prmtop and .rst7 files for each system.

  File Details:

  • Rigid target inputs:
    • target_min.prmtop, target_min.rst7
  • Flexible target inputs:
    • target.prmtop, target.rst7

GIST_Input_files

This folder contains:

• GIST input files for 34 systems.
• The topology and trajectory files for rigid and flexible systems were used as inputs, respectively.

Site_analysis_tools

This folder contains:

• Python code to analyze binding sites.
• Number of hydrogen bonds, Number of water neighbors, Conformation analysis of residues.