PLUMED 2: New feathers for an old bird

Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, +2

Computer Physics Communications

Avian LocomotionAvian EvolutionNew Feathers

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

Massimiliano Bonomi, Davide Branduardi, Giovanni Bussi, +8

Computer Physics Communications

EngineeringPhysicsNatural SciencesMolecular ComputingComputational Chemistry +4

From A to B in free energy space

Davide Branduardi, Francesco Luigi Gervasio, Michele Parrinello

The Journal of Chemical Physics

Infinite Dimensional AnalysisEngineeringMolecular BiologyFree Energy SpaceComputational Chemistry +15

Metadynamics with Adaptive Gaussians

Davide Branduardi, Giovanni Bussi, Michele Parrinello

Journal of Chemical Theory and Computation

Computational ScienceGaussian PotentialsEngineeringData ScienceGaussian Process +10

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

Anna Berteotti, Andrea Cavalli, Davide Branduardi, +3

Journal of the American Chemical Society

Nucleotide-dependent conformational states of actin

Jim Pfaendtner, Davide Branduardi, Michele Parrinello, +2

Proceedings of the National Academy of Sciences

Cleft WidthProtein AssemblyBiochemistryProtein FoldingBiophysics +13

The Role of the Peripheral Anionic Site and Cation−π Interactions in the Ligand Penetration of the Human AChE Gorge

Davide Branduardi, Francesco Luigi Gervasio, Andrea Cavalli, +2

Journal of the American Chemical Society

The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

Massimiliano Bonomi, Davide Branduardi, Francesco Luigi Gervasio, +1

Journal of the American Chemical Society

Protein AssemblyMolecular BiologyProtein RefoldingFolding MechanismMolecular Dynamics +15

A Catalytic Mechanism for Cysteine N-Terminal Nucleophile Hydrolases, as Revealed by Free Energy Simulations

Alessio Lodola, Davide Branduardi, Marco De Vivo, +4

PLoS ONE

Amide HydrolysisMedicinal ChemistryCatalytic MechanismAldo-keto ReductaseBiochemistry +12

Investigating the Mechanism of Substrate Uptake and Release in the Glutamate Transporter Homologue Glt_Ph through Metadynamics Simulations

Giovanni Grazioso, Vittorio Limongelli, Davide Branduardi, +4

Journal of the American Chemical Society

Biophysical ModelingSynaptic TransmissionNeurotransmitterMolecular BiologyNeurotransmission +18