The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems - Sorbonne Université Access content directly
Journal Articles Journal of Chemical Information and Modeling Year : 2023

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 non-covalent interaction networks. Owing to the large size of proteins, the analysis of their non-covalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The NCI [1-3] (non-covalent interaction) 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 non-covalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this 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.
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Dates and versions

hal-04198110 , version 1 (08-09-2023)

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Trinidad Novoa, Rubén Laplaza, Francesca Peccati, Franck Fuster, Julia Contreras-García. The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems. Journal of Chemical Information and Modeling, 2023, 63 (15), pp.4483-4489. ⟨10.1021/acs.jcim.3c00271⟩. ⟨hal-04198110⟩
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