Examples

Here you can find a representation of almost all the types of calculations and analyses that you can perform with xBFreE. Although each example focuses on specific cases, you can use xBFreE on systems that combine a number of different components (i.e. metalloprotein-ligand complex, Protein-DNA-ligand, etc.). In addition, several types of calculations (e.g. GB, Alanine scanning and Per-residue decomposition; PB, Interaction Entropy, and Per-wise decomposition) can be also performed in the same run for a specific system.

Systems¶

This is a representation of the systems that can be processed and analyzed with xBFreE. Our program has a robust method to process input structures. Even if your system is not represented here, still have a go, you won't be disappointed! 😀

• Protein-protein¹²³

Analysis¶

This section focuses on the analysis that can be performed with xBFreE. Although each example focuses on specific cases, you can use xBFreE to perform several types of calculations (e.g. GB, Alanine scanning and Per-residue decomposition; PB, Interaction Entropy, and Per-residue decomposition) in the same run for a specific system.

• Single Trajectory Protocol¹²³

• Binding free energy calculations

  • Binding free energy calculation with GB