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Interpreting solution X-ray scattering data using molecular simulations

Current opinion in structural biology, 2018-04, Vol.49, p.18-26

Hub, Jochen S

2018

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Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005800-e1005800

2017

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WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

Nucleic acids research, 2015-07, Vol.43 (W1), p.W225-W230

2015

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Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

Biophysical journal, 2014-07, Vol.107 (2), p.435-447

2014

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Free energies of membrane stalk formation from a lipidomics perspective

Nature communications, 2021-11, Vol.12 (1), p.6594-6594, Article 6594

2021

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Interpretation of Solution X-Ray Scattering by Explicit-Solvent Molecular Dynamics

Biophysical journal, 2015-05, Vol.108 (10), p.2573-2584

2015

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g_whamA Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Journal of chemical theory and computation, 2010-12, Vol.6 (12), p.3713-3720

2010

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DNA opening during transcription initiation by RNA polymerase II in atomic detail

Biophysical journal, 2022-11, Vol.121 (22), p.4299-4310

2022

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Simulations of Pore Formation in Lipid Membranes: Reaction Coordinates, Convergence, Hysteresis, and Finite-Size Effects

Journal of chemical theory and computation, 2016-07, Vol.12 (7), p.3261-3269

2016

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Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

Biophysical journal, 2013-12, Vol.105 (12), p.2760-2770

2013

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Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

Journal of chemical theory and computation, 2012-01, Vol.8 (1), p.61-74

2012

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Three- and four-site models for heavy water: SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW

The Journal of chemical physics, 2021-05, Vol.154 (19), p.194501-194501

2021

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Mechanism of selectivity in aquaporins and aquaglyceroporins

Proceedings of the National Academy of Sciences - PNAS, 2008-01, Vol.105 (4), p.1198-1203

2008

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Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs

The Journal of chemical physics, 2016-09, Vol.145 (12), p.125101-125101

2016

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Atomistic simulation of ion solvation in water explains surface preference of halides

Proceedings of the National Academy of Sciences - PNAS, 2011-04, Vol.108 (17), p.6838-6842

2011

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Detection of functional modes in protein dynamics

PLoS computational biology, 2009-08, Vol.5 (8), p.e1000480-e1000480

2009

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Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1

Biophysical journal, 2012-08, Vol.103 (4), p.786-796

2012

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Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

Proceedings of the National Academy of Sciences - PNAS, 2016-09, Vol.113 (38), p.10565-10570

2016

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Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc

PloS one, 2018-05, Vol.13 (5), p.e0196751-e0196751

2018

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Atomistic ensemble of active SHP2 phosphatase

Communications biology, 2023-12, Vol.6 (1), p.1289-1289, Article 1289

2023

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Hairpin protein partitioning from the ER to lipid droplets involves major structural rearrangements

Nature communications, 2024-05, Vol.15 (1), p.4504-4504, Article 4504

2024

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Combined Small-Angle X‑ray and Neutron Scattering Restraints in Molecular Dynamics Simulations

Journal of chemical theory and computation, 2019-08, Vol.15 (8), p.4687-4698

2019

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Molecular Anatomy of a Trafficking Organelle

Cell, 2006-11, Vol.127 (4), p.831-846

2006

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Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet

Computational and structural biotechnology journal, 2024-12, Vol.23, p.1169-1180

2024

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Structural Properties of Protein–Detergent Complexes from SAXS and MD Simulations

The journal of physical chemistry letters, 2015-12, Vol.6 (24), p.5116-5121

2015

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Interpreting solution X-ray scattering data using molecular simulations

Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

Free energies of membrane stalk formation from a lipidomics perspective

Interpretation of Solution X-Ray Scattering by Explicit-Solvent Molecular Dynamics

g_whamA Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

DNA opening during transcription initiation by RNA polymerase II in atomic detail

Simulations of Pore Formation in Lipid Membranes: Reaction Coordinates, Convergence, Hysteresis, and Finite-Size Effects

Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

Three- and four-site models for heavy water: SPC/E-HW, TIP3P-HW, and TIP4P/2005-HW

Mechanism of selectivity in aquaporins and aquaglyceroporins

Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs

Atomistic simulation of ion solvation in water explains surface preference of halides

Detection of functional modes in protein dynamics

Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc

Atomistic ensemble of active SHP2 phosphatase

Hairpin protein partitioning from the ER to lipid droplets involves major structural rearrangements

Combined Small-Angle X‑ray and Neutron Scattering Restraints in Molecular Dynamics Simulations

Molecular Anatomy of a Trafficking Organelle

Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet

Structural Properties of Protein–Detergent Complexes from SAXS and MD Simulations

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