Canan 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.

The paper uses molecular dynamics simulations to evaluate and rank the performance of single fluorescent protein-based calcium biosensors based on water distribution and hydrogen bond changes.

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.

The paper uses molecular dynamics simulations to analyze hydrogen bond dynamics in a maltose biosensor, identifying key factors distinguishing its bright and dark states.

This study investigates heterodimer formation among ZBTB transcription factors, confirming physical interactions and co-expression in immune cells, and analyzing energetic determinants of homo and heterodimer formation.

The paper reports the crystal structures of the PATZ1 BTB domain in mice and zebrafish, revealing its homodimeric structure and unique features in the dimerization interface.

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

This study uses computational methods to analyze how ATP and ADP affect the conformational dynamics of human Hsp90, identifying key residues involved in allosteric modulation.