Recent work in molecular simulation.

Journal of the American Chemical Society · 148 (28), 30494–30511

Nature Counts to Three: Universal Mg-Pinch Motif Polarizes the Cleaved Bond in NTP-Processing Enzymes

Bálint Dudás · Dénes Berta · Pablo Jambrina · Pedro J. Buigues · Reynier Suardíaz · Silvia Gómez-Coca · Wenhao Deng · Bernard R. Brooks · Beáta G. Vértessy · Edina Rosta

A cross-superfamily structural analysis identifies a conserved Mg²⁺ coordination motif flanking the scissile P–O bond; embedded DFT QM/MM calculations resolve its role in electrostatic preorganisation and reaction-induced polarisation.

Journal of Chemical Information and Modeling · 66 (3), 1566–1581

CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2

Oleksandra Herasymenko · Madhushika Silva · Gregory J. Correy · and the CACHE consortium, including Edina Rosta

Advances in Quantum Chemistry

QM/MM Free Energy Calculations for Enzyme Catalytic Reactions

Edina Rosta

ACS Catalysis · 15 (12), 10176–10187

Reaction Mechanism and Metal Selectivity of Human SAMHD1 Elucidated by QM/MM Calculations

Wen-Hao Deng · Harry Lewin · Rong-Zhen Liao · Edina Rosta

Journal of Chemical Theory and Computation

Quantifying Cooperativity through Binding Free Energies in Molecular Glue Degraders

Balint Dudas · Christina Athanasiou · Juan Carlos Mobarec · Edina Rosta

Journal of Chemical Information and Modeling · 65 (13), 6884–6898

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13

Oleksandra Herasymenko · Madhushika Silva · Abd Al-Aziz A. Abu-Saleh · and the CACHE consortium, including Dénes Berta, Daniel Felföldi, Sam Martino and Edina Rosta

Nature Methods

The Need to Implement FAIR Principles in Biomolecular Simulations

Rommie E. Amaro · Johan Åqvist · Ivet Bahar · and the biomolecular simulation community, including Edina Rosta

The Journal of Physical Chemistry B

Kemeny Constant-Based Optimization of Network Clustering Using Graph Neural Networks

Sam A. Martino · João Morado · C. Li · Z. Lu · Edina Rosta

Nature Communications

Uncovering Low-Frequency Vibrations in Surface-Enhanced Raman of Organic Molecules

A. Boehmke Amoruso · Rubén A. Boto · E. Elliot · Bart de Nijs · R. Esteban · Tamás Földes · F. Aguilar-Galindo · Edina Rosta · J. Aizpurua · Jeremy J. Baumberg

The Journal of Physical Chemistry Letters

Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method

Zsuzsanna Koczor-Benda · Teodora Mateeva · Edina Rosta

Journal of the American Chemical Society

Mechanism-Based Redesign of GAP to Activate Oncogenic Ras

Dénes Berta · Sascha Gehrke · Kinga Nyíri · Beáta G. Vértessy · Edina Rosta

Journal of Chemical Theory and Computation

Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor

Pedro J. Buigues · Sascha Gehrke · Magd Badaoui · Bálint Dudás · and collaborators · Edina Rosta

Nature Communications

Strong Structuring Arising from Weak Cooperative O–H···π and C–H···O Hydrogen Bonding in Benzene–Methanol Solution

Camilla Di Mino and collaborators · including Edina Rosta

Biochemical Journal

Dynamic Regulation of RAS and RAS Signaling

Walter Kolch · Dénes Berta · Edina Rosta

Small

SERS Sensing of Dopamine with Fe(III)-Sensitized Nanogaps in Recleanable AuNP Monolayer Films

M. Niihori · Tamás Földes · C. A. Readman · R. Arul · and collaborators · Edina Rosta · Jeremy J. Baumberg