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HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations

Physical chemistry chemical physics : PCCP, 2017, Vol.19 (48), p.32421-32432

2017

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Targeting Intrinsically Disordered Proteins through Dynamic Interactions

Biomolecules (Basel, Switzerland), 2020-05, Vol.10 (5), p.743

2020

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Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins

PLoS computational biology, 2012-01, Vol.8 (1), p.e1002353-e1002353

2012

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Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009567-e1009567

2021

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Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011460-e1011460

2023

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Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions

Physical chemistry chemical physics : PCCP, 2008-01, Vol.10 (4), p.471-481

2008

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Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing

PloS one, 2011-07, Vol.6 (7), p.e22837

2011

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Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields

Journal of chemical theory and computation, 2019-08, Vol.15 (8), p.4708-4720

2019

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Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations

Journal of chemical theory and computation, 2023-03, Vol.19 (5), p.1602-1614

2023

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Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models

Journal of chemical theory and computation, 2014-03, Vol.10 (3), p.918-923

2014

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Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels

The Journal of chemical physics, 2020-09, Vol.153 (11), p.110901-110901

2020

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Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models

Journal of chemical theory and computation, 2010-09, Vol.6 (9), p.2790-2803

Chen, Jianhan

2010

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Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions

Journal of chemical theory and computation, 2013-06, Vol.9 (6), p.2849-2856

2013

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Application of solid-state NMR restraint potentials in membrane protein modeling

Journal of magnetic resonance (1997), 2008-07, Vol.193 (1), p.68-76

2008

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Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding

Journal of chemical theory and computation, 2019-10, Vol.15 (10), p.5169-5174

2019

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Progress on the two-dimensional filter diagonalization method. An efficient doubling scheme for two-dimensional constant-time NMR

Journal of magnetic resonance (1997), 2003-05, Vol.162 (1), p.74-89

2003

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Conformational Flexibility and pH Effects on Anisotropic Growth of Sheet-Like Assembly of Amphiphilic Peptides

Journal of nanoscience and nanotechnology, 2015-06, Vol.15 (6), p.4470-4479

2015

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An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

Journal of chemical theory and computation, 2009-10, Vol.5 (10), p.2909-2923

2009

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RRT: The Regularized Resolvent Transform for High-Resolution Spectral Estimation

Journal of magnetic resonance (1997), 2000-11, Vol.147 (1), p.129-137

2000

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Regularization of the Two-Dimensional Filter Diagonalization Method: FDM2K

Journal of magnetic resonance (1997), 2000-10, Vol.146 (2), p.363-368

2000

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Multiscale filter diagonalization method for spectral analysis of noisy data with nonlocalized features

The Journal of chemical physics, 2000-03, Vol.112 (10), p.4429-4437

2000

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Ultra-high resolution 3D NMR spectra from limited-size data sets

Journal of magnetic resonance (1997), 2004-08, Vol.169 (2), p.215-224

2004

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Regularized resolvent transform for direct calculation of 45 degrees projections of 2D J spectra

Journal of magnetic resonance (1997), 2003-09, Vol.164 (1), p.136-144

2003

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Computing Energy Levels by Inversion of Imaginary-Time Cross-Correlation Functions

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2003-09, Vol.107 (37), p.7175-7180

2003

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Separation induced low-frequency unsteadiness in a supersonic combustor with single-side expansion

Physics of fluids (1994), 2019-05, Vol.31 (5)

2019

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HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations

Targeting Intrinsically Disordered Proteins through Dynamic Interactions

Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins

Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones

Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions

Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing

Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields

Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations

Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models

Hydrophobic dewetting in gating and regulation of transmembrane protein ion channels

Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions

Application of solid-state NMR restraint potentials in membrane protein modeling

Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding

Progress on the two-dimensional filter diagonalization method. An efficient doubling scheme for two-dimensional constant-time NMR

Conformational Flexibility and pH Effects on Anisotropic Growth of Sheet-Like Assembly of Amphiphilic Peptides

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

RRT: The Regularized Resolvent Transform for High-Resolution Spectral Estimation

Regularization of the Two-Dimensional Filter Diagonalization Method: FDM2K

Multiscale filter diagonalization method for spectral analysis of noisy data with nonlocalized features

Ultra-high resolution 3D NMR spectra from limited-size data sets

Regularized resolvent transform for direct calculation of 45 degrees projections of 2D J spectra

Computing Energy Levels by Inversion of Imaginary-Time Cross-Correlation Functions

Separation induced low-frequency unsteadiness in a supersonic combustor with single-side expansion

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