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

Surfaces is also offered as a Python package.

Tip

Now you can run Surfaces within PyMOL 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