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 <https://www.biorxiv.org/content/10.1101/2025.01.23.634566v1>`_.


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 <https://academic.oup.com/bioinformatics/article/39/10/btad608/7288175>`_.


.. toctree::
   :maxdepth: 2
   :caption: Index

   How_to_install
   Preprocessing
   Protein-protein
   Protein-ligand
   Particular_residues
   Customizations
   How_to_uninstall