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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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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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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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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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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.1338-1346

2012

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

Nucleic acids research, 2016-08, Vol.44 (14), p.6599-6613

2016

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Molecular Modeling in Drug Design

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

2019

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Identification of antiparasitic drug targets using a multi-omics workflow in the acanthocephalan model

BMC genomics, 2022-09, Vol.23 (1), p.1-677, Article 677

2022

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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.619-15, Article 619

2023

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Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Frontiers in molecular biosciences, 2019-05, Vol.6, p.36-36

2019

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Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations

Current research in structural biology, 2021-01, Vol.3, p.106-111

2021

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Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19

International journal of molecular sciences, 2019-09, Vol.20 (18), p.4328

2019

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The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms

The Journal of biological chemistry, 2022-02, Vol.298 (2), p.101507-101507, Article 101507

2022

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Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

eLife, 2022-07, Vol.11

2022

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Editorial: The Journal of Molecular Recognition: Changing of the guard

Journal of molecular recognition, 2024-05, Vol.37 (3), p.e3081-n/a

Wade, Rebecca C.

2024

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An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

Communications biology, 2021-01, Vol.4 (1), p.55-13, Article 55

2021

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MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I

Frontiers in immunology, 2022-10, Vol.13, p.930590-930590

2022

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The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity

PloS one, 2012-04, Vol.7 (4), p.e34870-e34870

2012

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A Bittersweet Computational Journey among Glycosaminoglycans

Biomolecules (Basel, Switzerland), 2021-05, Vol.11 (5), p.739

2021

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Recent progress in molecular simulation methods for drug binding kinetics

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

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

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

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

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

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

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

Molecular Modeling in Drug Design

Identification of antiparasitic drug targets using a multi-omics workflow in the acanthocephalan model

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

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations

Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19

The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

Editorial: The Journal of Molecular Recognition: Changing of the guard

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity

A Bittersweet Computational Journey among Glycosaminoglycans

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