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Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

PLoS computational biology, 2010-03, Vol.6 (3), p.e1000694-e1000694

2010

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Orientationally Averaged Version of the Rotne–Prager–Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules

Journal of chemical theory and computation, 2023-08, Vol.19 (15), p.5099-5111

2023

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Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

Journal of chemical theory and computation, 2013-09, Vol.9 (9), p.4176-4185

2013

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Optimizing Solute–Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements

Journal of chemical theory and computation, 2016-04, Vol.12 (4), p.1401-1407

2016

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Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome

Journal of molecular biology, 2022-01, Vol.434 (2), p.167377-167377, Article 167377

2022

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Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

Biophysical journal, 2010-11, Vol.99 (9), p.L75-L77

2010

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Molecular Dynamics Simulations of Hydrophobic Associations in Aqueous Salt Solutions Indicate a Connection between Water Hydrogen Bonding and the Hofmeister Effect

Journal of the American Chemical Society, 2007-12, Vol.129 (48), p.14887-14898

2007

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Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore

ACS nano, 2015-09, Vol.9 (9), p.9050-9061

2015

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Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

Journal of chemical theory and computation, 2009-02, Vol.5 (2), p.242-256

2009

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Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

Current opinion in structural biology, 2010-04, Vol.20 (2), p.196-206

Elcock, Adrian H

2010

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The Native 3D Organization of Bacterial Polysomes

Cell, 2009-01, Vol.136 (2), p.261-271

2009

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Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome

PLoS computational biology, 2006-07, Vol.2 (7), p.e98-e98

2006

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Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Nature structural & molecular biology, 2018-03, Vol.25 (3), p.279-288

2018

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Flexibility of the Bacterial Chaperone Trigger Factor in Microsecond-Timescale Molecular Dynamics Simulations

Biophysical journal, 2013-08, Vol.105 (3), p.732-744

2013

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Computational Sampling of a Cryptic Drug Binding Site in a Protein Receptor: Explicit Solvent Molecular Dynamics and Inhibitor Docking to p38 MAP Kinase

Journal of molecular biology, 2006-05, Vol.359 (1), p.202-214

2006

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Computer simulations of the bacterial cytoplasm

Biophysical reviews, 2013-06, Vol.5 (2), p.109-119

2013

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Improving signal and transit peptide predictions using AlphaFold2-predicted protein structures

Journal of molecular biology, 2024-01, Vol.436 (2), p.168393-168393, Article 168393

2024

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AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes

Structure (London), 2024-05, Vol.32 (5), p.621-629.e5

2024

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spotter : a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes

Nucleic acids research, 2023-09, Vol.51 (17), p.e92-e92

2023

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Direct Measurement of the Kinetics and Thermodynamics of Association of Hydrophobic Molecules from Molecular Dynamics Simulations

The journal of physical chemistry letters, 2011-01, Vol.2 (1), p.19-24

2011

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Dynamic binding of replication protein a is required for DNA repair

Nucleic acids research, 2016-07, Vol.44 (12), p.5758-5772

2016

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Structure Prediction of Large RNAs with AlphaFold3 Highlights its Capabilities and Limitations

Journal of molecular biology, 2024-11, Vol.436 (22), p.168816, Article 168816

2024

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Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome

Nucleic acids research, 2017-07, Vol.45 (13), p.7541-7554

2017

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Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

Chemical reviews, 2014-07, Vol.114 (13), p.6661-6714

2014

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Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides

Journal of chemical theory and computation, 2015-05, Vol.11 (5), p.2341-2354

2015

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Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

Orientationally Averaged Version of the Rotne–Prager–Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules

Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

Optimizing Solute–Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements

Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome

Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

Molecular Dynamics Simulations of Hydrophobic Associations in Aqueous Salt Solutions Indicate a Connection between Water Hydrogen Bonding and the Hofmeister Effect

Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

The Native 3D Organization of Bacterial Polysomes

Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Flexibility of the Bacterial Chaperone Trigger Factor in Microsecond-Timescale Molecular Dynamics Simulations

Computational Sampling of a Cryptic Drug Binding Site in a Protein Receptor: Explicit Solvent Molecular Dynamics and Inhibitor Docking to p38 MAP Kinase

Computer simulations of the bacterial cytoplasm

Improving signal and transit peptide predictions using AlphaFold2-predicted protein structures

AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes

spotter : a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes

Direct Measurement of the Kinetics and Thermodynamics of Association of Hydrophobic Molecules from Molecular Dynamics Simulations

Dynamic binding of replication protein a is required for DNA repair

Structure Prediction of Large RNAs with AlphaFold3 Highlights its Capabilities and Limitations

Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides

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