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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Nature methods, 2017-01, Vol.14 (1), p.71

2017

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Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

The journal of physical chemistry. B, 2017-08, Vol.121 (34), p.8009-8025

2017

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Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments

Physical chemistry chemical physics : PCCP, 2019-01, Vol.21 (2), p.876-883

2019

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Reduced efficacy of a Src kinase inhibitor in crowded protein solution

Nature communications, 2021-07, Vol.12 (1), p.4099-4099, Article 4099

2021

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Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments

eLife, 2021-01, Vol.10

2021

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Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

The Journal of chemical physics, 2014-03, Vol.140 (9), p.095101-095101

2014

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Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields

Journal of physical chemistry. C, 2014-06, Vol.118 (24), p.12929-12943

2014

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Amino acids and proteins at ZnO―water interfaces in molecular dynamics simulations

Physical chemistry chemical physics : PCCP, 2013-08, Vol.15 (32), p.13628-13636

2013

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Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

Proceedings of the National Academy of Sciences - PNAS, 2019-12, Vol.116 (49), p.24562-24567

2019

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Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

The journal of physical chemistry. B, 2017-12, Vol.121 (49), p.11072-11084

2017

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Proteins Near Solid Surfaces and at Air-Water Interfaces

Biophysical journal, 2016-02, Vol.110 (3), p.645a-645a

2016

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Liver transplantation for nonresectable metastatic solid pseudopapillary pancreatic cancer

Annals of transplantation, 2013-11, Vol.18, p.651

2013

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Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions

The journal of physical chemistry. B, 2022-12, Vol.126 (48), p.10256-10272

2022

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Amino acids and proteins at ZnOwater interfaces in molecular dynamics simulationsElectronic supplementary information (ESI) available: Characterization of the electrostatic potential generated by the studied surfaces, characterization of the structure of water near the surfaces, details of the umbrella sampling method, plots of the potentials of the mean force, and examples of three adsorption events. See DOI: 10.1039/c3cp52198b

2013-07

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Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions

Journal of the American Chemical Society, 2023-11, Vol.145 (43), p.23620-23629

2023

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Combining Force Fields and Neural Networks for an Accurate Representation of Bonded Interactions

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2024-02, Vol.128 (4), p.807-812

2024

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The Determination of Free Energy of Hydration of Water Ions from First Principles

Journal of chemical theory and computation, 2024-06, Vol.20 (12), p.5215-5224

2024

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Protein Diffusion in a Dense Solution Studied by All-Atom Molecular Dynamics Simulations

Biophysical journal, 2018-02, Vol.114 (3), p.233a-234a

2018

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Neural Network Corrections to Intermolecular Interaction Terms of a Molecular Force Field Capture Nuclear Quantum Effects in Calculations of Liquid Thermodynamic Properties

Journal of chemical theory and computation, 2024-02, Vol.20 (3), p.1347-1357

2024

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Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments

Journal of physics. Conference series, 2018-06, Vol.1036 (1), p.12010

2018

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Protein–Ligand Binding Free-Energy Calculations with ARROWA Purely First-Principles Parameterized Polarizable Force Field

Journal of chemical theory and computation, 2022-12, Vol.18 (12), p.7751-7763

2022

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Peptide Recognition Capabilities of Cellulose in Molecular Dynamics Simulations

Journal of physical chemistry. C, 2015-10, Vol.119 (43), p.24404-24416

2015

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Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It

Biophysical journal, 2018-10, Vol.115 (7), p.1190-1199

2018

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Accurate determination of solvation free energies of neutral organic compounds from first principles

Nature communications, 2022-01, Vol.13 (1), p.414-414, Article 414

2022

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Preoperative radiotherapy and local excision of rectal cancer with immediate radical re-operation for poor responders: A prospective multicentre study

Radiotherapy and oncology, 2013-02, Vol.106 (2), p.198-205

2013

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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments

Reduced efficacy of a Src kinase inhibitor in crowded protein solution

Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments

Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields

Amino acids and proteins at ZnO―water interfaces in molecular dynamics simulations

Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Proteins Near Solid Surfaces and at Air-Water Interfaces

Liver transplantation for nonresectable metastatic solid pseudopapillary pancreatic cancer

Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions

Combining Force Fields and Neural Networks for an Accurate Representation of Bonded Interactions

The Determination of Free Energy of Hydration of Water Ions from First Principles

Protein Diffusion in a Dense Solution Studied by All-Atom Molecular Dynamics Simulations

Neural Network Corrections to Intermolecular Interaction Terms of a Molecular Force Field Capture Nuclear Quantum Effects in Calculations of Liquid Thermodynamic Properties

Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments

Protein–Ligand Binding Free-Energy Calculations with ARROWA Purely First-Principles Parameterized Polarizable Force Field

Peptide Recognition Capabilities of Cellulose in Molecular Dynamics Simulations

Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It

Accurate determination of solvation free energies of neutral organic compounds from first principles

Preoperative radiotherapy and local excision of rectal cancer with immediate radical re-operation for poor responders: A prospective multicentre study

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