Added NCIPLOT to the alphabetical listing of applications. NCI (Non-Covalent Interactions) is a visualization index based on the density and its derivatives. It enables identification of non-covalent interactions. NCIPLOT is available for download.
Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc. 2010, 132, pp 6498-6506.
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. N. Beratan, and W. Yang. J. Chem. Theory Comput. 2011, 7, pp 625-632.