The NonCovalent Interaction index
(NCI) enables identification
of attractive and repulsive noncovalent interactions from promolecular
densities in a fast manner. However, the approach remained up to now
qualitative, only providing visual information. We present a new version
of NCIPLOT, NCIPLOT4, which allows quantifying the properties of the
NCI regions (volume, charge) in small and big systems in a fast manner.
Examples are provided of how this new twist enables characterization
and retrieval of local information in supramolecular chemistry and
biosystems at the static and dynamic levels.
Noncovalent interactions are of utmost importance. However, their accurate treatment is still difficult. This is partially induced by the coexistence of many types of interactions and physical phenomena, which hampers generality in simple treatments. The NCI index has been successfully used for nearly over 10 years in order to identify, analyze, and understand noncovalent interactions in a wide variety of systems, ranging from proteins to molecular crystals. In this work, the development and implications of the method will be reviewed, and modern implementations will be presented. Afterward, some sophisticated examples will be given that showcase the current advances toward the fast, robust, and intuitive identification of noncovalent interactions in real space.
This article is categorized under:
Software > Molecular Modeling
Quantum Computing > Theory Development
Structure and Mechanism > Computational Biochemistry and Biophysics
In this article we derive a complete characterization of the Solvent Excluded Surface (SES) for molecular systems including a complete characterization of singularities of the surface. The theory is based on an implicit representation of the SES, which, in turn, is based on the signed distance function to the Solvent Accessible Surface (SAS). All proofs are constructive so that the theory allows for efficient algorithms in order to compute the area of the SES and the volume of the SES-cavity, or to visualize the surface. Further, we propose to refine the notion of SAS and SES in order to take inner holes in a solute molecule into account or not.
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