Proteins rarely have a function on their own. Their biological activities are driven by specific and non-specific interactions with other biomolecules such as proteins and nucleic acids. Understanding these interactions is central to uncovering the mechanisms underlying cellular processes and developing pharmacological strategies.  Recent advances in experimental structural biology, such as cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), nuclear magnetic resonance (NMR) spectroscopy, and X-ray crystallography, have yielded high-resolution static structures of protein complexes. However, the dynamical mechanisms governing how proteins recognize and bind to their partners remain an outstanding scientific challenge. We develop and implement advanced computational chemistry methods and multiscale models to study long-timescale biomolecular interactions over a broad resolution range (from atomistic description of biological systems to highly coarse-grained models).

Selected Publications

Banerjee P. et al. (2024) "Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding". Biophysical Journal, 123, 42.

Banerjee P. et al. (2024) "Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation", Biophysical Journal, 123, 389.

Banerjee P. et al. (2020) "Dynamical control by water at a molecular level in protein dimer association and dissociation", Proc. Natl. Acad. Sci. 117(5), 2302.

Banerjee P. et al. (2019) "Effect of ethanol on insulin dimer dissociation" J. Chem. Phys. 150, 084902.

Banerjee P. et al. (2018) "Insulin dimer dissociation in aqueous solution: A computational study of free energy landscape and evolving microscopic structure along the reaction pathway", J. Chem. Phys. 149, 114902.