Surfaces’ documentation

Surfaces comprises a collection of Python scripts that provide a rapid means to assess protein interactions by analyzing the atomic surface areas in contact and the types of atoms involved in the interaction.

Tip

Now you can run Surfaces as part of the NRGSuite-Qt plugin.

In this document, we offer a guide on how to install and utilize the protein-protein and protein-ligand interaction evaluation functions, as well as the evaluation function of all the interactions associated with specific residues of interest. We also provide a manual for utilizing the structure preprocessing scripts necessary for each of these functions.

Note

Cite this work as Surfaces: A software to quantify and visualise interactions within and between proteins and ligands.

Index

• How to install
• Preprocessing
  • Structure files
  • Protein structures
  • Ligands
  • Modeled structures
• Protein-Protein
  • Interaction calculation
  • Visual output
  • Example application
• Protein-Ligand
  • Interaction calculation
  • Visual output
  • Example application
• Particular residues
  • Interaction calculation
  • Visual output
  • Example application
• Customizations
  • Atom type definitions
  • Pairwise interaction
  • Visual outputs
  • Scaling factor
• How to uninstall