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Journal Articles

Configurational entropy, transition rates, and optimal interactions for rapid folding in coarse-grained model proteins

Margarita Colberg, Jeremy Schofield
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 125101 (2022)
https://doi.org/10.1063/5.0098612
Published: September 2022
View article titled, Configurational entropy, transition rates, and optimal interactions for rapid folding in coarse-grained model proteins
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Journal Articles

Computing transition path theory quantities with trajectory stratification

Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 034106 (2022)
https://doi.org/10.1063/5.0087058
Published: July 2022
View article titled, Computing transition path theory quantities with trajectory stratification
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Includes: Supplementary data
Journal Articles

Nucleic acid folding simulations using a physics-based atomistic free energy model

Chi H. Mak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 174114 (2022)
https://doi.org/10.1063/5.0086304
Published: May 2022
View article titled, Nucleic acid folding simulations using a physics-based atomistic free energy model
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Journal Articles

Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders

Mahdi Ghorbani, Samarjeet Prasad, Jeffery B. Klauda, Bernard R. Brooks
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 194108 (2021)
https://doi.org/10.1063/5.0069708
Published: November 2021
View article titled, Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders
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Includes: Supplementary data
Journal Articles

CORE-MD II: A fast, adaptive, and accurate enhanced sampling method

Emanuel K. Peter, Dietmar J. Manstein, Joan-Emma Shea, Alexander Schug
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 104114 (2021)
https://doi.org/10.1063/5.0063664
Published: September 2021
View article titled, CORE-MD II: A fast, adaptive, and accurate enhanced sampling method
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Journal Articles

Unfolding bovine α -lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations

Darren J. Hsu, Denis Leshchev, Irina Kosheleva, Kevin L. Kohlstedt, Lin X. Chen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 105101 (2021)
https://doi.org/10.1063/5.0039194
Published: March 2021
View article titled, Unfolding bovine <em>α</em> -lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations
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Includes: Supplementary data
Journal Articles

Thermal versus mechanical unfolding in a model protein

Rafael Tapia-Rojo, Juan J. Mazo, Fernando Falo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 185105 (2019)
https://doi.org/10.1063/1.5126071
Published: November 2019
View article titled, Thermal versus mechanical unfolding in a model protein
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Journal Articles

Folding pathways of NuG2—a designed mutant of protein G—using relaxation mode analysis

Ayori Mitsutake, Hiroshi Takano
Journal: The Journal of Chemical Physics
J. Chem. Phys. 151, 044117 (2019)
https://doi.org/10.1063/1.5097708
Published: July 2019
View article titled, Folding pathways of NuG2—a designed mutant of protein G—using relaxation mode analysis
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Journal Articles

Dynamical coring of Markov state models

Daniel Nagel, Anna Weber, Benjamin Lickert, Gerhard Stock
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 094111 (2019)
https://doi.org/10.1063/1.5081767
Published: March 2019
View article titled, Dynamical coring of Markov state models
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Includes: Supplementary data
Journal Articles

Assessment and optimization of collective variables for protein conformational landscape: GB1 β-hairpin as a case study

Navjeet Ahalawat, Jagannath Mondal
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 094101 (2018)
https://doi.org/10.1063/1.5041073
Published: September 2018
View article titled, Assessment and optimization of collective variables for protein conformational landscape: GB1 <em>β</em>-hairpin as a case study
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Includes: Supplementary data
Journal Articles

Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length, and macromolecular crowding

Phuong Thuy Bui, Trinh Xuan Hoang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 045102 (2018)
https://doi.org/10.1063/1.5033361
Published: July 2018
View article titled, Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length, and macromolecular crowding
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Includes: Supplementary data
Journal Articles

The folding pathways and thermodynamics of semiflexible polymers

Jing Wu, Chenqian Cheng, Gaoyuan Liu, Ping Zhang, Tao Chen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 184901 (2018)
https://doi.org/10.1063/1.5018114
Published: May 2018
View article titled, The folding pathways and thermodynamics of semiflexible polymers
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Includes: Supplementary data
Journal Articles

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

Hiranmay Maity, Govardhan Reddy
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 165101 (2018)
https://doi.org/10.1063/1.5022632
Published: April 2018
View article titled, Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L
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Includes: Supplementary data
Journal Articles

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

Tristan Cragnolini, Debayan Chakraborty, Jiří Šponer, Philippe Derreumaux, Samuela Pasquali, David J. Wales
Journal: The Journal of Chemical Physics
J. Chem. Phys. 147, 152715 (2017)
https://doi.org/10.1063/1.4997377
Published: August 2017
View article titled, Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch
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Includes: Supplementary data
Journal Articles

Structural entanglements in protein complexes

Yani Zhao, Mateusz Chwastyk, Marek Cieplak
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 225102 (2017)
https://doi.org/10.1063/1.4985221
Published: June 2017
View article titled, Structural entanglements in protein complexes
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Includes: Supplementary data
Journal Articles

The effects of tether placement on antibody stability on surfaces

Rebecca W. Grawe, Thomas A. Knotts, IV
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 215102 (2017)
https://doi.org/10.1063/1.4983705
Published: June 2017
View article titled, The effects of tether placement on antibody stability on surfaces
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Journal Articles

On the polymer physics origins of protein folding thermodynamics

Mark P. Taylor, Wolfgang Paul, Kurt Binder
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 174903 (2016)
https://doi.org/10.1063/1.4966645
Published: November 2016
View article titled, On the polymer physics origins of protein folding thermodynamics
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Journal Articles

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

Agnieszka G. Lipska, Steven R. Seidman, Adam K. Sieradzan, Artur Giełdoń, Adam Liwo, Harold A. Scheraga
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 184110 (2016)
https://doi.org/10.1063/1.4948710
Published: May 2016
View article titled, Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction
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Includes: Supplementary data
Journal Articles

Modelling DNA origami self-assembly at the domain level

Frits Dannenberg, Katherine E. Dunn, Jonathan Bath, Marta Kwiatkowska, Andrew J. Turberfield, Thomas E. Ouldridge
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 165102 (2015)
https://doi.org/10.1063/1.4933426
Published: October 2015
View article titled, Modelling DNA origami self-assembly at the domain level
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Journal Articles

Folding of small knotted proteins: Insights from a mean field coarse-grained model

Saeed Najafi, Raffaello Potestio
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 243121 (2015)
https://doi.org/10.1063/1.4934541
Published: October 2015
View article titled, Folding of small knotted proteins: Insights from a mean field coarse-grained model
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Includes: Supplementary data