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Full-Text Articles in Physical Sciences and Mathematics
From Isotropic To Anisotropic Side Chain Representations: Comparison Of Three Models For Residue Contact Estimation, Weitao Sun, Jing He
From Isotropic To Anisotropic Side Chain Representations: Comparison Of Three Models For Residue Contact Estimation, Weitao Sun, Jing He
Computer Science Faculty Publications
The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the C-alpha-to-C-alpha atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the …