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Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

Reports on progress in physics, 2008-12, Vol.71 (12), p.126601

2008

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Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

Journal of the American Chemical Society, 2016-11, Vol.138 (43), p.14257-14263

2016

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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

Accounts of chemical research, 2020-03, Vol.53 (3), p.654-661

2020

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Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies

Journal of chemical theory and computation, 2020-07, Vol.16 (7), p.4641-4654

2020

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Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

PLoS computational biology, 2015-11, Vol.11 (11), p.e1004578

2015

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Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor

The journal of physical chemistry letters, 2019-04, Vol.10 (8), p.1928-1934

2019

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Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells

Biochemical journal, 2018-06, Vol.475 (11), p.1909-1937

2018

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TRPC1 binds to caveolin-3 and is regulated by Src kinase - role in Duchenne muscular dystrophy

Journal of cell science, 2008-07, Vol.121 (13), p.2246-2255

2008

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Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

Cell chemical biology, 2016-10, Vol.23 (10), p.1193-1205

2016

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The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers

Nature communications, 2018-10, Vol.9 (1), p.4325-17, Article 4325

2018

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N-Acetylcysteine ameliorates skeletal muscle pathophysiology in mdx mice

The Journal of physiology, 2008-04, Vol.586 (7), p.2003-2014

2008

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Drug-resistant EGFR mutations promote lung cancer by stabilizing interfaces in ligand-free kinase-active EGFR oligomers

Nature communications, 2024-03, Vol.15 (1), p.2130-2130, Article 2130

2024

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Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

eLife, 2017-04, Vol.6

2017

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Patient autoantibodies deplete postsynaptic muscle‐specific kinase leading to disassembly of the ACh receptor scaffold and myasthenia gravis in mice

The Journal of physiology, 2010-09, Vol.588 (17), p.3217-3229

2010

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Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

Accounts of chemical research, 2015-02, Vol.48 (2), p.277-285

2015

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Using metadynamics and path collective variables to study ligand binding and induced conformational transitions

Methods in molecular biology (Clifton, N.J.), 2012-01, Vol.819, p.501

2012

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Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer

Cells (Basel, Switzerland), 2019-04, Vol.8 (4), p.316

2019

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Defining an Optimal Metric for the Path Collective Variables

Journal of chemical theory and computation, 2019-01, Vol.15 (1), p.25-32

2019

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Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

Journal of chemical theory and computation, 2012-04, Vol.8 (4), p.1165-1170

2012

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Monitoring genotoxicity among gasoline station attendants and traffic enforcers in the City of Manila using the micronucleus assay with exfoliated epithelial cells

Environmental monitoring and assessment, 2009-09, Vol.156 (1-4), p.331-341

2009

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The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion

PLoS computational biology, 2014-10, Vol.10 (10), p.e1003863

2014

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Pathways of Ca²⁺ entry and cytoskeletal damage following eccentric contractions in mouse skeletal muscle

Journal of applied physiology (1985), 2012-06, Vol.112 (12), p.2077-2086

2012

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Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained

Chemistry : a European journal, 2009-08, Vol.15 (32), p.7913-7921

2009

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Structural basis of connexin-36 gap junction channel inhibition

Cell discovery, 2024-06, Vol.10 (1), p.68-4

2024

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Activated Actin-Depolymerizing Factor/Cofilin Sequesters Phosphorylated Microtubule-Associated Protein during the Assembly of Alzheimer-Like Neuritic Cytoskeletal Striations

The Journal of neuroscience, 2009-10, Vol.29 (41), p.12994-13005

2009

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Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor

Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells

TRPC1 binds to caveolin-3 and is regulated by Src kinase - role in Duchenne muscular dystrophy

Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers

N-Acetylcysteine ameliorates skeletal muscle pathophysiology in mdx mice

Drug-resistant EGFR mutations promote lung cancer by stabilizing interfaces in ligand-free kinase-active EGFR oligomers

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Patient autoantibodies deplete postsynaptic muscle‐specific kinase leading to disassembly of the ACh receptor scaffold and myasthenia gravis in mice

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

Using metadynamics and path collective variables to study ligand binding and induced conformational transitions

Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer

Defining an Optimal Metric for the Path Collective Variables

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

Monitoring genotoxicity among gasoline station attendants and traffic enforcers in the City of Manila using the micronucleus assay with exfoliated epithelial cells

The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion

Pathways of Ca²⁺ entry and cytoskeletal damage following eccentric contractions in mouse skeletal muscle

Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained

Structural basis of connexin-36 gap junction channel inhibition

Activated Actin-Depolymerizing Factor/Cofilin Sequesters Phosphorylated Microtubule-Associated Protein during the Assembly of Alzheimer-Like Neuritic Cytoskeletal Striations

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