Krishnakanth Baratam

Exploring the Energy Landscape of Hairpin Folding using the TIS-DNA model

This paper uses the TIS-DNA model to study DNA hairpin folding, showing it quantitatively describes thermodynamics and recapitulates kinetic features like multiple pathways.

Phosphoinositides protonation states dictate AKT1 binding with membrane

This study shows that phosphoinositide protonation microstates determine AKT1 membrane binding specificity and how mutations alter this interaction.

Dose-Dependent Softening of Bacterial Model Membranes by Structurally Distinct Antimicrobial Peptides: A Coarse-Grained Molecular Dynamics Study

This paper uses molecular dynamics simulations to show how different antimicrobial peptides alter membrane mechanical properties in a dose-dependent manner, with structured peptides causing greater softening than disordered ones.

Division of labor in cargo and membrane recognition by SNX1-SNX5: Insights from multiscale modelling

This paper uses multiscale modeling to investigate how SNX1-SNX5 heterodimers recognize cargo and membranes in a retromer-independent manner.

SOP-MULTI: A self-organized polymer based coarse-grained model for multi-domain and intrinsically disordered proteins with conformation ensemble consistent with experimental scattering data

The paper introduces SOP-MULTI, a coarse-grained force field for simulating multi-domain and intrinsically disordered proteins, validated against experimental scattering data.