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

Abstract

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein–protein and protein–ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server () accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

Mechanism of cationic ring-opening polymerisation of ε-caprolactone using metallocene/borate catalytic systems: a DFT and NCI study on chain initiation, propagation and termination

“…To analyse the nature of interactions present between the cationic zirconocene species and the counteranions during the CL CROP, non-covalent interaction (NCI) analysis 48,49 is performed on important reaction intermediates and transition states using the NCIweb server ( ). 50 Contreras-Garcia et al have recently introduced this user-friendly platform to study NCIs, based on the analysis of electron density, ρ , and reduced density gradient, s (also referred to as RDG), according to the eqn (1) . In this NCIweb calculation, the promolecular density approximation is used, 51 and only an input structure (PDB, XYZ or WFN format) is required for each job submission.…”