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Journal Articles

ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

Viet Thanh Duy Nguyen, Nhan D. Nguyen, Truong Son Hy
Journal: Structural Dynamics
Struct. Dyn. 11, 064102 (2024)
https://doi.org/10.1063/4.0000271
Published: November 2024
View article titled, ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models
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Journal Articles

Local photo-mechanical stiffness revealed in gold nanoparticles supracrystals by ultrafast small-angle electron diffraction

Editor’s Pick
Giulia Fulvia Mancini, Francesco Pennacchio, Tatiana Latychevskaia, Javier Reguera, Francesco Stellacci, Fabrizio Carbone
Journal: Structural Dynamics
Struct. Dyn. 6, 024304 (2019)
https://doi.org/10.1063/1.5091858
Published: April 2019
View article titled, Local photo-mechanical stiffness revealed in gold nanoparticles supracrystals by ultrafast small-angle electron diffraction
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Includes: Supplementary data
Journal Articles

Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Kyle M. Stiers, Abigail C. Graham, Jian-She Zhu, David L. Jakeman, Jay C. Nix, Lesa J. Beamer
Journal: Structural Dynamics
Struct. Dyn. 6, 024703 (2019)
https://doi.org/10.1063/1.5092803
Published: April 2019
View article titled, Structural and dynamical description of the enzymatic reaction of a phosphohexomutase
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Includes: Supplementary data
Journal Articles

The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction

Yuchen Li, Yalong Cong, Guoqiang Feng, Susu Zhong, John Z. H. Zhang, Huiyong Sun, Lili Duan
Journal: Structural Dynamics
Struct. Dyn. 5, 064101 (2018)
https://doi.org/10.1063/1.5058172
Published: December 2018
View article titled, The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction
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Includes: Supplementary data
Journal Articles

Preface to Swiss National Center of Competence in Research: Molecular Ultrafast Science and Technology

Thomas Feurer, Ursula Keller
Journal: Structural Dynamics
Struct. Dyn. 4, 061401 (2017)
https://doi.org/10.1063/1.5018454
Published: January 2018
View article titled, Preface to Swiss National Center of Competence in Research: Molecular Ultrafast Science and Technology
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Journal Articles

Charge migration and charge transfer in molecular systems

Hans Jakob Wörner, Christopher A. Arrell, Natalie Banerji, Andrea Cannizzo, Majed Chergui, Akshaya K. Das, Peter Hamm, Ursula Keller, Peter M. Kraus, Elisa Liberatore, Pablo Lopez-Tarifa, Matteo Lucchini, Markus Meuwly, Chris Milne, Jacques-E. Moser, Ursula Rothlisberger, Grigory Smolentsev, Joël Teuscher, Jeroen A. van Bokhoven, Oliver Wenger
Journal: Structural Dynamics
Struct. Dyn. 4, 061508 (2017)
https://doi.org/10.1063/1.4996505
Published: December 2017
View article titled, Charge migration and charge transfer in molecular systems
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Journal Articles

Implications of short time scale dynamics on long time processes

Krystel El Hage, Sebastian Brickel, Sylvain Hermelin, Geoffrey Gaulier, Cédric Schmidt, Luigi Bonacina, Siri C. van Keulen, Swarnendu Bhattacharyya, Majed Chergui, Peter Hamm, Ursula Rothlisberger, Jean-Pierre Wolf, Markus Meuwly
Journal: Structural Dynamics
Struct. Dyn. 4, 061507 (2017)
https://doi.org/10.1063/1.4996448
Published: December 2017
View article titled, Implications of short time scale dynamics on long time processes
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Journal Articles

Ultrafast kinetics of linkage isomerism in Na2[Fe(CN)5NO] aqueous solution revealed by time-resolved photoelectron spectroscopy

Azhr A. Raheem, Martin Wilke, Mario Borgwardt, Nicholas Engel, Sergey I. Bokarev, Gilbert Grell, Saadullah G. Aziz, Oliver Kühn, Igor Yu. Kiyan, Christoph Merschjann, Emad F. Aziz
Journal: Structural Dynamics
Struct. Dyn. 4, 044031 (2017)
https://doi.org/10.1063/1.4990567
Published: June 2017
View article titled, Ultrafast kinetics of linkage isomerism in Na<sub>2</sub>[Fe(CN)<sub>5</sub>NO] aqueous solution revealed by time-resolved photoelectron spectroscopy
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Journal Articles

Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2′-bipyridine)2(CN)2]

Kasper S. Kjær, Wenkai Zhang, Roberto Alonso-Mori, Uwe Bergmann, Matthieu Chollet, Ryan G. Hadt, Robert W. Hartsock, Tobias Harlang, Thomas Kroll, Katharina Kubiček, Henrik T. Lemke, Huiyang W. Liang, Yizhu Liu, Martin M. Nielsen, Joseph S. Robinson, Edward I. Solomon, Dimosthenis Sokaras, Tim B. van Driel, Tsu-Chien Weng, Diling Zhu, Petter Persson, Kenneth Wärnmark, Villy Sundström, Kelly J. Gaffney
Journal: Structural Dynamics
Struct. Dyn. 4, 044030 (2017)
https://doi.org/10.1063/1.4985017
Published: June 2017
View article titled, Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2′-bipyridine)<sub>2</sub>(CN)<sub>2</sub>]
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Includes: Supplementary data
Journal Articles

Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation

Nita R. Shah, Craig Wilkinson, Steven P. D. Harborne, Ainoleena Turku, Kun-Mou Li, Yuh-Ju Sun, Sarah Harris, Adrian Goldman
Journal: Structural Dynamics
Struct. Dyn. 4, 032105 (2017)
https://doi.org/10.1063/1.4978038
Published: March 2017
View article titled, Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation
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Journal Articles

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

Hongnan Cao, Kemin Tan, Fengbin Wang, Lance Bigelow, Ragothaman M. Yennamalli, Robert Jedrzejczak, Gyorgy Babnigg, Craig A. Bingman, Andrzej Joachimiak, Madan K. Kharel, Shanteri Singh, Jon S. Thorson, George N. Phillips, Jr.
Journal: Structural Dynamics
Struct. Dyn. 3, 034702 (2016)
https://doi.org/10.1063/1.4948539
Published: April 2016
View article titled, Structural dynamics of a methionine <em>γ</em>-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate
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Includes: Supplementary data
Journal Articles

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V. Dokholyan, Charles W. Carter, Jr.
Journal: Structural Dynamics
Struct. Dyn. 3, 012101 (2016)
https://doi.org/10.1063/1.4941599
Published: February 2016
View article titled, A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms
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Journal Articles

Ligand and interfacial dynamics in a homodimeric hemoglobin

Prashant Kumar Gupta, Markus Meuwly
Journal: Structural Dynamics
Struct. Dyn. 3, 012003 (2016)
https://doi.org/10.1063/1.4940228
Published: February 2016
View article titled, Ligand and interfacial dynamics in a homodimeric hemoglobin
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