Ali Rana Atılgan

The paper introduces a temporal hydrogen-bond network analysis framework to study ligand-directed connectivity in DHFR, revealing mutation-sensitive pathways and evolutionarily supported communication regions.

The paper uses simulations to identify CaM conformations under different calcium and salt conditions, showing how these factors influence its conformational dynamics.

The paper introduces a method to identify key residues driving conformational changes in proteins using multiple perturbations, with applications in biosensor design.

This study uses thermodynamic cycles and FEP simulations to predict the effects of resistance mutations on DHFR's competitive inhibition with TMP, revealing structural and dynamical impacts on enzyme function.

The paper demonstrates the feasibility of high-throughput mutational scanning of a protein using alchemical free energy calculations on a high-performance computing resource.

This study investigates TolC protein dynamics in Gram-negative bacteria, identifying structural shifts that facilitate β-lactam efflux and resistance, with implications for antibiotic design.

The paper uses computational methods to analyze the mutational landscape of GB1's binding to IgG-Fc, identifying key hydrogen bonds and structural features that influence binding affinity.

MODE-TASK provides tools for analyzing protein motion using molecular dynamics and normal mode analysis techniques.