Dynamical Redesign of Biomolecular Networks

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

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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