#4 · Structural bio & protein design

Ensemble and free-energy methods now resolve RNA, protein and ligand binding physics

The dominant thread is physically grounded sampling and energetics of biomolecular conformations rather than single static models. mdRNAcat curates all-atom REST2 replica-exchange MD for 48 RNA systems in standardized HDF5. gmx_MMPBSA adds GBNSR6 and nonlinear PB models, C2 entropy and AMBER support for end-state binding free energies. P-RISE identifies force field, ionic, dielectric and entropy requirements for reliable RNA-ligand prediction. What is new is the emphasis on reusable ensemble resources and on explicit determination of which physical terms govern reliability. The quantum-walk study on protein contact networks is a non-MD complement rather than part of this trend.