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First, we generate optimal pairwise interface alignments and then use a version of the neighbor-joining algorithm to align multiple interfaces.
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All pairwise comparisons of interfaces are separated into two groups according to whether the corresponding complexes are S/D-homologous or non-homologous.
The other two replacements also participate in cross-interface pairwise and third-order epistatic interactions.
To demonstrate the approach, we solve for all ground states for a binary alloy in a 2D hexagonal lattice both with and without an interface, based on pairwise interactions.
Williams, C. D. et al. Effective polarization in pairwise potentials at the graphene electrolyte interface.
This is important because true protein complexes must admit a topology of pairwise binding at the level of interfaces, and these interfaces are often exclusive (Aloy and Russell, 2006; Kim et al., 2006).
Next, we derived the interfaces similarity by pairwise comparison using the Pearson's correlation coefficient (PCC).
Short-range pairwise interactions between sites across the interface hold together the bound complex.
For the three-layer structure with sand-mixture interlayer, constraint strains in the interface were determined on pairwise comparison.
In this article, we introduce a polynomial-time algorithm for optimal pairwise contact map alignment of protein interfaces using two-dimensional (2D) dynamic programming.
The nonpolar solvation energy GGBSUR is approximated by a pairwise potential that occurs at the incompatible interface of two distinct species molecules.
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