Aysima Hacisuleyman

The paper characterizes SNARE-like proteins from Heimdallarchaeota, showing their four-helix bundle structure and evolutionary relationship to eukaryotic SNARE complexes.

The paper introduces an alphabet of allostery using transfer entropy to predict allosteric-site character and conformational rewiring across proteins.

The paper uses Hodge decomposition to analyze information flow in KRAS proteins, showing that mutations reposition information sources while maintaining a hierarchical flow structure.

The paper introduces a pattern-matching strategy to predict protein contact maps from sequences, achieving high correlation with experimental data using minimal computational resources.

This paper designs light-regulated dynamic proteins using deep learning, showing precise optogenetic control of cellular processes.

This study uses molecular dynamics simulations to show how the G12D mutation in KRAS increases entropy and dynamic coupling, altering its conformational landscape and function.

This paper introduces a method using mutual information profile shifts to assess the pathogenicity of Pyrin mutations in familial Mediterranean fever, showing how negative shifts indicate severe functional effects.

The paper investigates the structural arrangement of SNARE proteins in QabcR complexes and shows that structural exchange is tolerated but some non-cognate exchanges lead to imbalances.

This study identifies a camelid single-domain antibody that allosterically inhibits trypanosomatid pyruvate kinases, reducing parasite growth.

The paper develops a sequence-based method to create 2D contact maps and analyze conserved allosteric hot spots in protein domains without requiring GPUs.

The paper evaluates ZDOCK decoys for nanobody-protein complexes using the Dreiding Force Field, finding translations sufficient for accurate docking and identifying salt bridges as essential for recognition.

The paper quantifies information transfer between protein residues using transfer entropy, showing significant long-range information transfer and high transfer rates in PSD-95.