Martin Zacharias

The paper introduces SACCELERATOR, a framework for spatially aware clustering that improves benchmarking by incorporating expert feedback and consensus analysis across diverse datasets.

The paper identifies a DNA-bound intermediate during MCM2-7 helicase activation and shows how DNA unwinding is coupled to helicase complex disassembly and DNA exit.

This study develops a method to estimate protein melting temperatures using small-ladder replica exchange simulations, showing improved efficiency with iterative temperature ladders.

This study investigates how the p97/VCP mutation D395G increases redox sensitivity, leading to oxidative inactivation and contributing to neurodegeneration.

This paper uses coarse-grained simulations and reflectivity data to study RNA-lipid interactions at interfaces, showing how RNA structure affects binding and validating simulation results with experimental data.

This paper introduces AI-MCLig, a method for designing protein ligands that accounts for protein flexibility and conformational adaptation, achieving binding scores comparable to known binders.

This study uses cryo-EM, NMR, and MD simulations to reveal the atomic-level mechanism of ATP processing by p97, identifying a metastable ADP.Pi state and its role in coordinating subunit actions.

The paper investigates how the APP ectodomain regulates gamma-secretase processivity and A beta peptide length, identifying it as a target for Alzheimer's disease therapies.

The paper evaluates Zn2+ models in metalloproteins, finding that nonbonded models struggle while dummy-atom models perform best for octahedral coordination.

The paper identifies sequence preferences of TET enzymes that target DNA demethylation to bHLH and bZIP transcription factor binding sites.