When carbon gives way to silicon, the classic conformational analysis tools fall silent. Here is how we adapted one of structural biology's most iconic plots for a new class of polymers — and packaged it for anyone to use. The Ramachandran plot has guided structural biology for over sixty years. By mapping the two backbone dihedral angles φ and ψ for every residue in a protein, it reveals at a glance whether a structure is sterically plausible, which secondary structures are

At its core, MM-PBSA is a framework for estimating the thermodynamic potential of molecular association, grounded in the canonical ensemble of statistical mechanics. The binding of a ligand (L) to a receptor (R) to form a complex (RL) can be rigorously described by the Helmholtz free energy difference: ΔG_bind = G_RL - (G_R + G_L) = -k_B T ln(Z_RL / (Z_R Z_L)), where each Z is a configurational partition function integrating over all atomic coordinates and solvent degrees of

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Evolutionary game theory, where Darwinian selection meets strategic decision-making, is a powerful tool for understanding animal...