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Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

Current opinion in pharmacology, 2010-12, Vol.10 (6), p.738-744

Salsbury, Freddie R

2010

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Impact of A2T and D23N mutations on C99 homodimer conformations

The Journal of chemical physics, 2022-08, Vol.157 (8), p.085102-085102

2022

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Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods

Journal of chemical information and modeling, 2023-06, Vol.63 (12), p.3705-3718

2023

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Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer

The Journal of chemical physics, 2018-01, Vol.148 (4), p.045105-045105

2018

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Light Chain Mutation Effects on the Dynamics of Thrombin

Journal of chemical information and modeling, 2021-02, Vol.61 (2), p.950-965

2021

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Na + -binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling

Physical chemistry chemical physics : PCCP, 2019-02, Vol.21 (8), p.4320-4330

2019

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Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42)

The Journal of chemical physics, 2017-04, Vol.146 (14), p.145101-145101

2017

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Mechanistic insights into thrombin's switch between "slow" and "fast" forms

Physical chemistry chemical physics : PCCP, 2017-09, Vol.19 (36), p.24522-24533

2017

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Amyloid-β(29–42) Dimeric Conformations in Membranes Rich in Omega‑3 and Omega‑6 Polyunsaturated Fatty Acids

The journal of physical chemistry. B, 2019-03, Vol.123 (12), p.2687-2696

2019

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Simulations suggest double sodium binding induces unexpected conformational changes in thrombin

Journal of molecular modeling, 2022-05, Vol.28 (5), p.120-120, Article 120

2022

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TREX1 as a Novel Immunotherapeutic Target

Frontiers in immunology, 2021-04, Vol.12, p.660184-660184

2021

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New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

Journal of computational chemistry, 2003-08, Vol.24 (11), p.1348-1356

2003

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Constant-pH molecular dynamics using continuous titration coordinates

Proteins, structure, function, and bioinformatics, 2004-09, Vol.56 (4), p.738-752

2004

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Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

PloS one, 2016-02, Vol.11 (2), p.e0149014-e0149014

2016

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Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin

Journal of biomolecular structure & dynamics, 2017-11, Vol.35 (15), p.3354-3369

2017

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Experimentally Dissecting the Origins of Peroxiredoxin Catalysis

Antioxidants & redox signaling, 2018-03, Vol.28 (7), p.521

2018

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Substrate recognition and near-cognate discrimination by the wobble-base modifying enzyme tRNA-isoleucine lysidine synthase (TilS)

Biophysical journal, 2023-02, Vol.122 (3), p.216a-216a

2023

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Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge

Journal of chemical theory and computation, 2016-12, Vol.12 (12), p.6130-6146

2016

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Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

Journal of biomolecular structure & dynamics, 2019-03, Vol.37 (4), p.982-999

2019

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Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator)

Biochemistry (Easton), 2017-01, Vol.56 (4), p.623-633

2017

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Visualizing ensembles in structural biology

Journal of molecular graphics & modelling, 2016-06, Vol.67, p.44-53

2016

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Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

PloS one, 2015-11, Vol.10 (11), p.e0142774-e0142774

2015

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Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

Protein science, 2008-02, Vol.17 (2), p.299-312

2008

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Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation

PloS one, 2019-09, Vol.14 (9), p.e0222814-e0222814

2019

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A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

PloS one, 2019-07, Vol.14 (7), p.e0219473-e0219473

2019

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Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

Impact of A2T and D23N mutations on C99 homodimer conformations

Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods

Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer

Light Chain Mutation Effects on the Dynamics of Thrombin

Na + -binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling

Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42)

Mechanistic insights into thrombin's switch between "slow" and "fast" forms

Amyloid-β(29–42) Dimeric Conformations in Membranes Rich in Omega‑3 and Omega‑6 Polyunsaturated Fatty Acids

Simulations suggest double sodium binding induces unexpected conformational changes in thrombin

TREX1 as a Novel Immunotherapeutic Target

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations

Constant-pH molecular dynamics using continuous titration coordinates

Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin

Experimentally Dissecting the Origins of Peroxiredoxin Catalysis

Substrate recognition and near-cognate discrimination by the wobble-base modifying enzyme tRNA-isoleucine lysidine synthase (TilS)

Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge

Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator)

Visualizing ensembles in structural biology

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid

Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

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