NCIPLOT4 Guide for Biomolecules: An Analysis Tool for Noncovalent Interactions

This Application Note is a guide for the use of the NCIPLOT4 code in the analysis of noncovalent interactions in biomacromolecular systems. Through a series of examples, the reader is walked through the process of calculating and interpreting noncovalent interaction density integrals corresponding to attractive, van der Waals, and repulsive terms in protein-ligand and protein-protein interaction problems. These integrals are robust and powerful tools to quickly obtain a semiquantitative picture of noncovalent interactions in complex systems with a temporal resolution (along a trajectory) and allow a flexible factorization of the noncovalent interactions network that permits the simultaneous evaluation of a wide range of contacts. The NCIPLOT4 code is publicly available at https://github.com/juliacontrerasgarcia/nciplot .