The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems

Itis well-known that the activity and function of proteinsisstrictly correlated with their secondary, tertiary, and quaternarystructures. Their biological role is regulated by their conformationalflexibility and global fold, which, in turn, is largely governed bycomplex noncovalent interaction networks. Because of the large sizeof proteins, the analysis of their noncovalent interaction networksis challenging, but can provide insights into the energetics of conformationalchanges or protein-protein and protein-ligand interactions.The noncovalent interaction (NCI) index, based on the reduced densitygradient, is a well-established tool for the detection of weak contactsin biological systems. In this work, we present a web-based applicationto expand the use of this index to proteins, which only requires amolecular structure as input and provides a mapping of the number,type, and strength of noncovalent interactions. Structure preparationis automated and allows direct importing from the PDB database, makingthis server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics.A quick overview of this tool and concise instructions are presented,together with an illustrative application.

Automated summary

This study presents a web-based tool for analyzing the noncovalent interaction networks of proteins, providing insights into the energetics of conformational changes, protein-protein, and protein-ligand interactions. The tool automates structure preparation and allows direct importing from the PDB database, making it accessible to scientists with limited bioinformatics experience.