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Recent progress in molecular simulation methods for drug binding kinetics

Current opinion in structural biology, 2020-10, Vol.64, p.126-133

2020

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New approaches for computing ligand–receptor binding kinetics

Current opinion in structural biology, 2018-04, Vol.49, p.1-10

2018

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The Shape of Protein Crowders is a Major Determinant of Protein Diffusion

Biophysical journal, 2013-04, Vol.104 (7), p.1576-1584

2013

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A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

The Journal of chemical physics, 2020-09, Vol.153 (12), p.125102-125102

2020

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Chromatosome Structure and Dynamics from Molecular Simulations

Annual review of physical chemistry, 2020-04, Vol.71, p.101

2020

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Structure and dynamics of the membrane-bound cytochrome P450 2C9

PLoS computational biology, 2011-08, Vol.7 (8), p.e1002152-e1002152

2011

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Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification

Biophysical journal, 2018-05, Vol.114 (10), p.2363-2375

2018

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Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments

PLoS biology, 2018-07, Vol.16 (7), p.e2005345-e2005345

2018

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PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport

PLoS pathogens, 2023-06, Vol.19 (6), p.e1011436-e1011436

2023

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The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics

Scientific reports, 2020-04, Vol.10 (1), p.7284-7284, Article 7284

2020

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Contact Map Fingerprints of Protein–Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics

Journal of chemical theory and computation, 2021-10, Vol.17 (10), p.6522-6535

2021

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A tightly regulated molecular toggle controls AAA+ disaggregase

Nature structural & molecular biology, 2012-12, Vol.19 (12), p.1338

2012

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Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

PLoS computational biology, 2019-10, Vol.15 (10), p.e1007382-e1007382

2019

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The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

PLoS pathogens, 2018-09, Vol.14 (9), p.e1007315

2018

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DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study

Biophysical journal, 2021-09, Vol.120 (17), p.3747-3763

2021

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Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes

eLife, 2017-05, Vol.6

2017

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Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex

Journal of molecular biology, 2016-07, Vol.428 (14), p.2880-2897

2016

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Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics

Journal of chemical information and modeling, 2023-08, Vol.63 (15), p.4691-4707

2023

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Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

Biophysical journal, 2010-12, Vol.99 (11), p.3782-3791

2010

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Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

Nucleic acids research, 2016-08, Vol.44 (14), p.6599

2016

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An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration

Nature communications, 2023-02, Vol.14 (1), p.619-619, Article 619

2023

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When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces

Nano letters, 2015-11, Vol.15 (11), p.7508-7513

2015

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A unique profilin-actin interface is important for malaria parasite motility

PLoS pathogens, 2017-05, Vol.13 (5), p.e1006412-e1006412

2017

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Molecular Modeling in Drug Design

Molecules (Basel, Switzerland), 2019-01, Vol.24 (2), p.321

2019

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Recent progress in molecular simulation methods for drug binding kinetics

New approaches for computing ligand–receptor binding kinetics

The Shape of Protein Crowders is a Major Determinant of Protein Diffusion

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

Chromatosome Structure and Dynamics from Molecular Simulations

Structure and dynamics of the membrane-bound cytochrome P450 2C9

Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification

Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport

The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics

Contact Map Fingerprints of Protein–Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics

A tightly regulated molecular toggle controls AAA+ disaggregase

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex

Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics

Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration

When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces

A unique profilin-actin interface is important for malaria parasite motility

Molecular Modeling in Drug Design

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