Lista de obras -

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls

artículo científico publicado en 2022

Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein–Ligand Binding Affinities Dominated by Cation−π Interactions

scientific article published on 14 June 2021

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA.

artículo científico publicado en 2018

Addressing Polarization Phenomena in Molecular Machines Containing Transition Metal Ions with an Additive Force Field

scientific article published on 07 February 2019

Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane

scientific article published on 26 April 2019

Annexin-V stabilizes membrane defects by inducing lipid phase transition

scientific article published on 13 January 2020

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

artículo científico publicado en 2018

Changes in Microenvironment Modulate the B- to A-DNA Transition

scientific article published on 28 February 2019

Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I

artículo científico publicado en 2020

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases

artículo científico publicado en 2016

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD

scientific article published on 27 August 2019

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

artículo científico publicado en 2017

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

artículo científico publicado en 2018

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex

artículo científico publicado en 2020

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines

artículo científico publicado en 2018

Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water

scientific article published on 20 February 2019

Enzyme-mimetic self-catalyzed polymerization of polypeptide helices

scientific article published on 29 November 2019

Hazardous Shortcuts in Standard Binding Free Energy Calculations

artículo científico publicado en 2022

How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine

artículo científico publicado en 2018

Induced Night Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

scientific article published on 06 November 2019

Link between Membrane Composition and Permeability to Drugs

artículo científico publicado en 2018

Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases

scientific article published on 03 September 2019

Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

artículo científico publicado en 2019

Methodology for the Simulation of Molecular Motors at Different Scales

artículo científico publicado en 2016

Modulation of membrane permeability by carbon dioxide

scientific article published on 03 September 2019

Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi

scientific article published on 11 November 2019

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

artículo científico publicado en 2017

Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential

artículo científico publicado en 2021

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles.

artículo científico publicado en 2017

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.

artículo científico publicado en 2018

Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity.

artículo científico publicado en 2016

Repurposing Existing Molecular Machines through Accurate Regulation of Cooperative Motions

artículo científico publicado en 2020

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

artículo científico publicado en 2020

String Method for Protein-Protein Binding Free-Energy Calculations

artículo científico publicado en 2019

Taming Rugged Free Energy Landscapes Using an Average Force

scientific article published on 04 November 2019

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations.

artículo científico publicado en 2017

The lubricating role of water in the shuttling of rotaxanes

artículo científico publicado en 2017

Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations

artículo científico publicado en 2016

Tribute to Klaus Schulten.

artículo científico publicado en 2017

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

scientific article published in 2022

α-Helix Unwinding as Force Buffer in Spectrins

artículo científico publicado en 2018

Lista de obras de

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls

Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein–Ligand Binding Affinities Dominated by Cation−π Interactions

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA.

Addressing Polarization Phenomena in Molecular Machines Containing Transition Metal Ions with an Additive Force Field

Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane

Annexin-V stabilizes membrane defects by inducing lipid phase transition

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

Changes in Microenvironment Modulate the B- to A-DNA Transition

Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines

Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water

Enzyme-mimetic self-catalyzed polymerization of polypeptide helices

Hazardous Shortcuts in Standard Binding Free Energy Calculations

How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine

Induced Night Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

Link between Membrane Composition and Permeability to Drugs

Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases

Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

Methodology for the Simulation of Molecular Motors at Different Scales

Modulation of membrane permeability by carbon dioxide

Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.

Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity.

Repurposing Existing Molecular Machines through Accurate Regulation of Cooperative Motions

Scalable molecular dynamics on CPU and GPU architectures with NAMD ⬇️

String Method for Protein-Protein Binding Free-Energy Calculations

Taming Rugged Free Energy Landscapes Using an Average Force

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations.

The lubricating role of water in the shuttling of rotaxanes

Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations

Tribute to Klaus Schulten.

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

α-Helix Unwinding as Force Buffer in Spectrins