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Updated: Jan 24, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
Computational Protocol to Evaluate Side-Chain Vicinal Spin-Spin Coupling Constants and Karplus Equation in Amino
J San Fabián1, S Omar1, J M García de la Vega1
1Departamento de Química Física Aplicada, Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain.
Abstract:
A computational protocol has been applied to the alanine dipeptide model in order to study the side-chain conformation, the calculated spin-spin coupling constants involved in the side-chain χ1 angle, and theoretical extended Karplus equations developed for amino acids. Two structures within the backbone secondary conformation are used to predict coupling constants which in addition are employed to analyze the effect of those structures on the resulting Karplus extended equations. The number of Fourier coefficients to be included within the Karplus equations is critically analyzed. Wave function and density functional methods as well as different basis sets are compared to find appropriate Karplus coefficients in the most efficient way. The influence of exchange and correlation functionals and the solvent effect on the calculated couplings are considered.
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