Dynamical Redesign of Biomolecular Networks

Publications

Simulated tempering with irreversible Gibbs sampling techniques

Author(s): Fahim Faizi, Pedro J. Buigues, George Deligiannidis, Edina Rosta
Published in: The Journal of Chemical Physics, Issue 153/21, 2020, Page(s) 214111, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0025775

Optical probes of molecules as nano-mechanical switches

Author(s): Dean Kos, Giuliana Di Martino, Alexandra Boehmke, Bart de Nijs, Dénes Berta, Tamás Földes, Sara Sangtarash, Edina Rosta, Hatef Sadeghi, Jeremy J. Baumberg
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19703-y

Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor

Author(s): Pedro J. Buigues; Sascha Gehrke; Magd Badaoui; Balint Dudas; Gaurav Mandana; Tianyun Qi; Giovanni Bottegoni; Edina Rosta
Published in: Journal of Chemical Theory and Computation, Issue 3, 2023, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00023

Resolving sub-angstrom ambient motion through reconstruction from vibrational spectra

Author(s): Edina Rosta; Edina Rosta; Charlie Readman; Bart de Nijs; Tamás Földes; Tamás Földes; Jeremy J. Baumberg; Rohit Chikkaraddy; David-Benjamin Grys; Jack Griffiths; Dénes Berta; Dénes Berta; Demelza Wright; William M. Deacon
Published in: Nature Communications, Issue 3, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26898-1

The Role of Conserved Residues in the DEDDh Motif: the Proton-Transfer Mechanism of HIV-1 RNase H

Author(s): Simon L. Dürr; Simon L. Dürr; Olga Bohuszewicz; Dénes Berta; Reynier Suardíaz; Pablo G. Jambrina; Christine Peter; Yihan Shao; Edina Rosta; Edina Rosta
Published in: ACS Catalysis, Issue 1, 2021, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.1c01493

Host–Guest Chemistry Meets Electrocatalysis: Cucurbit[6]uril on a Au Surface as a Hybrid System in CO 2 Reduction

Author(s): Andreas Wagner, Khoa H. Ly, Nina Heidary, István Szabó, Tamás Földes, Khaleel I. Assaf, Steven J. Barrow, Kamil Sokołowski, Mohamed Al-Hada, Nikolay Kornienko, Moritz F. Kuehnel, Edina Rosta, Ingo Zebger, Werner M. Nau, Oren A. Scherman, Erwin Reisner
Published in: ACS Catalysis, Issue 10/1, 2019, Page(s) 751-761, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.9b04221

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

Author(s): Dénes Berta, Pedro J Buigues, Magd Badaoui, Edina Rosta
Published in: Current Opinion in Structural Biology, Issue 61, 2020, Page(s) 198-206, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2020.01.002

Dynamic regulation of RAS and RAS signaling

Author(s): Walter Kolch, Denes Berta, Edina Rosta
Published in: Biochemical Journal, 2023, ISSN 0264-6021
Publisher: Portland Press, Ltd.
DOI: 10.1042/bcj20220234

Toward Understanding CB[7]-Based Supramolecular Diels-Alder Catalysis

Author(s): Dénes Berta, István Szabó, Oren A. Scherman, Edina Rosta
Published in: Frontiers in Chemistry, Issue 8, 2020, ISSN 2296-2646
Publisher: Frontiers Media
DOI: 10.3389/fchem.2020.587084

Markov Models of Molecular Kinetics

Author(s): Frank Noé, Edina Rosta
Published in: The Journal of Chemical Physics, Issue 151/19, 2019, Page(s) 190401, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5134029

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design.

Author(s): Dénes Berta; Dénes Berta; Magd Badaoui; Magd Badaoui; Sam Alexander Martino; Sam Alexander Martino; Pedro J. Buigues; Pedro J. Buigues; Andrei V. Pisliakov; Nadia Elghobashi-Meinhardt; Geoff Wells; Sarah A. Harris; Elisa Frezza; Edina Rosta; Edina Rosta
Published in: Chemical Science, Issue 1, 2021, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1sc02775a

Molecular Vibration Explorer: an Online Database and Toolbox for Surface-Enhanced Frequency Conversion and Infrared and Raman Spectroscopy

Author(s): Koczor-Benda, Zsuzsanna; Roelli, Philippe; Galland, Christophe; Rosta, Edina
Published in: The Journal of Physical Chemistry A, Issue 5, 2022, ISSN 1089-5639
Publisher: American Chemical Society
DOI: 10.1021/acs.jpca.2c03700

Mechanistic study of an immobilized molecular electrocatalyst by in situ gap-plasmon-assisted spectro-electrochemistry

Author(s): Demelza Wright, Qianqi Lin, Dénes Berta, Tamás Földes, Andreas Wagner, Jack Griffiths, Charlie Readman, Edina Rosta, Erwin Reisner, Jeremy J Baumberg
Published in: Nature Catalysis, 2021, ISSN 2520-1158
Publisher: Nature Publishing Group
DOI: 10.1038/s41929-020-00566-x

In-Situ Spectro-Electrochemistry of Conductive Polymers Using Plasmonics to Reveal Doping Mechanisms

Author(s): Peng, Jialong; Paragon-Plus: 6354277; Lin, Qianqi; Paragon-Plus: 6354295; Földes, Tamás; Paragon-Plus: 6440701; Jeong, Hyeon-Ho; Paragon-Plus: 2970429; Xiong, Yuling; Paragon-Plus: 6354282; Pitsalidis, Charalampos; Paragon-Plus: 6354287; Malliaras, George G.; Paragon-Plus: 3634054; Rosta, Edina; Paragon-Plus: 1831730; Baumberg, Jeremy J.; Paragon-Plus: 919226
Published in: ACS Nano, Issue 9, 2022, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.17863/cam.92306

Efficient Irreversible Monte Carlo Samplers

Author(s): Fahim Faizi, George Deligiannidis, Edina Rosta
Published in: Journal of Chemical Theory and Computation, Issue 16/4, 2020, Page(s) 2124-2138, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b01135

Cucurbit[7]uril as a Supramolecular Artificial Enzyme for Diels-Alder Reactions

Author(s): Aniello Palma, Markus Artelsmair, Guanglu Wu, Xiaoyong Lu, Steven J. Barrow, Najib Uddin, Edina Rosta, Eric Masson, Oren A. Scherman
Published in: Angewandte Chemie International Edition, Issue 56/49, 2017, Page(s) 15688-15692, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201706487

Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis

Author(s): Lindsay McGregor, Tamás Földes, Soi Bui, Martine Moulin, Nicolas Coquelle, Matthew P. Blakeley, Edina Rosta, Roberto A. Steiner
Published in: IUCrJ, Issue 8/1, 2021, Page(s) 46-59, ISSN 2052-2525
Publisher: IUCrJ
DOI: 10.1107/s2052252520013615

Molecular Screening for Terahertz Detection with Machine-Learning-Based Methods

Author(s): Zsuzsanna Koczor-Benda; Alexandra L. Boehmke; Angelos Xomalis; Rakesh Arul; Charlie Readman; Jeremy J. Baumberg; Edina Rosta
Published in: Physical Review X, Issue 1, 2021, ISSN 2160-3308
Publisher: American Physical Society
DOI: 10.1103/physrevx.11.041035

Structural Dynamics and Catalytic Mechanism of ATP13A2 (PARK9) from Simulations.

Author(s): Teodora Mateeva; Marco Klähn; Edina Rosta; Edina Rosta
Published in: The Journal of Physical Chemistry B, Issue 1, 2021, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.1c05337

Mechanism-Based Redesign of GAP to Activate Oncogenic Ras

Author(s): Dénes Berta; Sascha Gehrke; Kinga Nyíri; Beáta G. Vértessy; Edina Rosta
Published in: Journal of the American Chemical Society, Issue 5, 2023, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c04330

Combined free energy calculation and machine learning methods for understanding ligand unbinding kinetics

Author(s): Magd Badaoui, Pedro J Buigues, Dénes Berta, Guarav M Mandana, Hankang Gu, Callum J Dickson, Viktor Hornak, Mitsunori Kato, Carla Molteni, Simon D Parsons, Edina Rosta
Published in: Journal of Chemical Theory and Computation, 2022, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.1c00924

Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis.

Author(s): François Sicard; François Sicard; Vladimir Koskin; Vladimir Koskin; Alessia Annibale; Edina Rosta; Edina Rosta
Published in: Journal of Chemical Theory and Computation, Issue 1, 2021, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01151

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

Author(s): Matthew Faulkner, István Szabó, Samantha L. Weetman, Francois Sicard, Roland G. Huber, Peter J. Bond, Edina Rosta, Lu-Ning Liu
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-74536-5

Variational kinetic clustering of complex networks

Author(s): Vladimir Koskin; Adam Kells; Joe Clayton; Alexander K. Hartmann; Alessia Annibale; Edina Rosta
Published in: The Journal of Chemical Physics, Issue 2, 2022, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0105099

Organocatalytic Access to a cis -Cyclopentyl-γ-amino Acid: An Intriguing Model of Selectivity and Formation of a Stable 10/12-Helix from the Corresponding γ/α-Peptide

Author(s): Rossana Fanelli, Dénes Berta, Tamás Földes, Edina Rosta, Robert Andrew Atkinson, Hans-Jörg Hofmann, Kenneth Shankland, Alexander J. A. Cobb
Published in: Journal of the American Chemical Society, Issue 142/3, 2020, Page(s) 1382-1393, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.9b10861

Breaking the selection rules of spin-forbidden molecular absorption in plasmonic nanocavities

Author(s): Oluwafemi S Ojambati, William M Deacon, Rohit Chikkaraddy, Charlie Readman, Qianqi Lin, Zsuzsanna Koczor-Benda, Edina Rosta, Oren A Scherman, Jeremy J Baumberg
Published in: ACS Photonics, 2020, ISSN 2330-4022
Publisher: American Chemical Society
DOI: 10.1021/acsphotonics.0c00732

Modular supramolecular dimerization of optically tunable extended aryl viologens

Author(s): Magdalena Olesińska, Guanglu Wu, Silvia Gómez-Coca, Daniel Antón-García, Istvan Szabó, Edina Rosta, Oren A. Scherman
Published in: Chemical Science, Issue 10/38, 2019, Page(s) 8806-8811, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc03057c

Mean first passage times in variational coarse graining using Markov state models

Author(s): Adam Kells, Zsuzsanna É. Mihálka, Alessia Annibale, Edina Rosta
Published in: The Journal of Chemical Physics, Issue 150/13, 2019, Page(s) 134107, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5083924

A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.

Author(s): Xiaoliang Pan; Kwangho Nam; Evgeny Epifanovsky; Andrew C. Simmonett; Edina Rosta; Yihan Shao
Published in: The Journal of Chemical Physics, Issue 1, 2021, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0038120

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

Author(s): Zsuzsanna Koczor-Benda, Teodora Mateeva, Edina Rosta
Published in: The Journal of Physical Chemistry Letters, 2023, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1021/acs.jpclett.3c02624

Structural basis of second-generation HIV integrase inhibitor action and viral resistance

Author(s): Nicola J. Cook, Wen Li, Dénes Berta, Magd Badaoui, Allison Ballandras-Colas, Andrea Nans, Abhay Kotecha, Edina Rosta, Alan N. Engelman, Peter Cherepanov
Published in: Science, Issue 367/6479, 2020, Page(s) 806-810, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aay4919

Combining data integration and molecular dynamics for target identification in α-Synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1 (Synj1)

Author(s): Kirsten Jenkins, Teodora Mateeva, István Szabó, Andre Melnik, Paola Picotti, Attila Csikász-Nagy, Edina Rosta
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 1032-1042, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.04.010

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

Author(s): Oleksii S. Rukhlenko, Fahimeh Khorsand, Aleksandar Krstic, Jan Rozanc, Leonidas G. Alexopoulos, Nora Rauch, Keesha E. Erickson, William S. Hlavacek, Richard G. Posner, Silvia Gómez-Coca, Edina Rosta, Cheree Fitzgibbon, David Matallanas, Jens Rauch, Walter Kolch, Boris N. Kholodenko
Published in: Cell Systems, Issue 7/2, 2018, Page(s) 161-179.e14, ISSN 2405-4712
Publisher: Elsevier
DOI: 10.1016/j.cels.2018.06.002

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations

Author(s): Xiaoliang Pan, Edina Rosta, Yihan Shao
Published in: Molecules, Issue 23/10, 2018, Page(s) 2500, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules23102500

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

Author(s): Sam Alexander Martino, João Morado, Chenghao Li, Zhenghao Lu, Edina Rosta
Published in: The Journal of Physical Chemistry B, Issue 128, 2024, Page(s) 8103-8115, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.3c08213

Optical suppression of energy barriers in single molecule-metal binding

Author(s): Lin, Qianqi; Hu, Shu; Földes, Tamás; Huang, Junyang; Wright, Demelza; Griffiths, Jack; Elliott, Eoin; de Nijs, Bart; Rosta, Edina; Baumberg, Jeremy J.
Published in: Science Advances, Issue 6, 2022, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abp9285

Detecting mid-infrared light by molecular frequency upconversion in dual-wavelength nanoantennas

Author(s): Angelos Xomalis, Xuezhi Zheng, Rohit Chikkaraddy, Zsuzsanna Koczor-Benda, Ermanno Miele, Edina Rosta, Guy AE Vandenbosch, Alejandro Martínez, Jeremy J Baumberg
Published in: Science, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abk2593

Correlation functions, mean first passage times, and the Kemeny constant

Author(s): Adam Kells, Vladimir Koskin, Edina Rosta, Alessia Annibale
Published in: The Journal of Chemical Physics, Issue 152/10, 2020, Page(s) 104108, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/1.5143504

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