List of works - Alessandro Laio

A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations.

scientific article published on 16 January 2013

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1.

scientific article

A Markov state modeling analysis of sliding dynamics of a 2D model.

scientific article published in October 2017

A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations

scientific article published on 10 May 2012

A QUICKSTEP-based quantum mechanics/molecular mechanics approach for silica

scientific article published on 01 April 2006

A Variational Definition of Electrostatic Potential Derived Charges

A comparative theoretical study of dipeptide solvation in water.

scientific article published in April 2006

A fingerprint of surface-tension anisotropy in the free-energy cost of nucleation

scientific article published in February 2013

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

scientific article published in August 2009

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

scientific article

A molecular spring for vision.

scientific article published in December 2004

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions

scientific article published in April 2005

A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels

scientific article published on 22 June 2015

Ab initio simulations of Lewis-acid-catalyzed hydrosilylation of alkynes

scientific article published on 01 September 2005

Absolute transition rates for rare events from dynamical decoupling of reaction variables

scientific article published on 12 October 2012

Advillin folding takes place on a hypersurface of small dimensionality

scientific article published on 10 November 2008

Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies

scientific article

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations.

scientific article published in September 2006

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling

scientific article published in November 2005

Anisotropy of Earth's D″ layer and stacking faults in the MgSiO3 post-perovskite phase

scientific article published in Nature

Are structural biases at protein termini a signature of vectorial folding?

scientific article published in January 2006

Assessing the Accuracy of Metadynamics†

scientific article published on 01 April 2005

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids

scientific article published on 01 October 2018

Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation

scientific article published on 20 November 2012

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching.

scientific article published in March 2007

Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

scientific article published in October 2004

Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories

scientific article published on 12 January 2018

Calculating thermodynamics properties of quantum systems by a non-Markovian Monte Carlo procedure

scientific article published on 21 July 2009

Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations

scientific article published on 11 December 2020

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

scientific article published on 9 April 2013

Charge Localization in DNA Fibers

scientific article published in Physical Review Letters

Computational design of cyclic peptides for the customized oriented immobilization of globular proteins

scientific article published on 6 January 2017

Computing the Free Energy without Collective Variables

scientific article published on 19 February 2018

Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations.

scientific article

Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study

scientific article published in February 2008

Correlations among hydrogen bonds in liquid water

scientific article published on 16 August 2004

Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions

scientific article

Deciphering the folding kinetics of transmembrane helical proteins

scientific article published in December 2000

Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.

scientific article published on 23 September 2015

Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach.

scientific article published on 28 February 2012

Dissociation mechanism of acetic acid in water

scientific article published on 01 September 2006

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

scientific article published on 9 June 2003

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

scientific article published in March 2006

Equilibrium Free Energies from Nonequilibrium Metadynamics

scientific article published in Physical Review Letters

Escaping free-energy minima

scientific article

Estimating the intrinsic dimension of datasets by a minimal neighborhood information.

scientific article published on 22 September 2017

Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its Cα Carbons

scientific article published on 20 December 2019

Exploring the universe of protein structures beyond the Protein Data Bank

scientific article (publication date: 2010)

Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer

scientific article published on 03 February 2011

Flexible docking in solution using metadynamics

scientific article

Force generation in lamellipodia is a probabilistic process with fast growth and retraction events.

scientific article

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics

scientific article published in October 2006

Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide

scientific article published on 15 June 2016

Influence of DNA structure on the reactivity of the guanine radical cation

scientific article published in October 2004

Initial stages of salt crystal dissolution determined with ab initio molecular dynamics

article

Machine learning. Clustering by fast search and find of density peaks.

scientific article published in June 2014

Markov state modeling of sliding friction. ⬇️

scientific article published on 2 November 2016

Metadynamics convergence law in a multidimensional system

scientific article published on 07 May 2010

Metadynamics simulations reveal a Na+ independent exiting path of galactose for the inward-facing conformation of vSGLT

scientific article

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

Microscopic Mechanism of Antibiotics Translocation through a Porin

scientific article published on July 2004

Multidimensional view of amyloid fibril nucleation in atomistic detail.

scientific article

Native fold and docking pose discrimination by the same residue-based scoring function.

scientific article published on 5 February 2015

New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods.

scientific article published on 20 September 2017

Non-Markovian effects on protein sequence evolution due to site dependent substitution rates

scientific article

Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model.

scientific article published in March 2010

Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment

scientific article published on 14 September 2017

Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations

scientific article published on 20 July 2016

Physics of iron at Earth's core conditions

scientific article published in February 2000

Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms

scientific article

Predicting Crystal Structures: The Parrinello-Rahman Method Revisited

scientific article published in Physical Review Letters

Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations

scientific article published on 23 July 2019

Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants.

scientific article published on 13 October 2007

Preface: Special Topic on Enhanced Sampling for Molecular Systems

scientific article published on 01 August 2018

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

scientific article

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

scientific article published in August 2003

Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4.

scientific article published on 11 March 2016

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

scientific article published on 5 August 2016

Shape and area fluctuation effects on nucleation theory ⬇️

scientific article published on 01 March 2014

Spontaneously Forming Dendritic Voids in Liquid Water Can Host Small Polymers

scientific article published on 06 September 2019

Systematic improvement of classical nucleation theory

scientific article published on 30 May 2012

The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein–Protein Interactions

scientific article published on 18 March 2019

The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases

scientific article (publication date: 5 September 2007)

The energy gap as a universal reaction coordinate for the simulation of chemical reactions

scientific article published on 01 June 2009

The intrinsic dimension of protein sequence evolution

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

scientific article

The permeation mechanism of organic cations through a CNG mimic channel

scholarly article by Luisa M R Napolitano published in August 2018

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition

scientific article published on 01 June 2018

Tracing the Entropy along a Reactive Pathway: The Energy As a Generalized Reaction Coordinate

scientific article published on 01 September 2009

Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes.

scientific article published on 10 January 2018

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

article

fMRI single trial discovery of spatio-temporal brain activity patterns.

scientific article published on 23 November 2016

List of works by Alessandro Laio

A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations.

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1.

A Markov state modeling analysis of sliding dynamics of a 2D model.

A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations

A QUICKSTEP-based quantum mechanics/molecular mechanics approach for silica

A Variational Definition of Electrostatic Potential Derived Charges

A comparative theoretical study of dipeptide solvation in water.

A fingerprint of surface-tension anisotropy in the free-energy cost of nucleation

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

A molecular spring for vision.

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions

A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels

Ab initio simulations of Lewis-acid-catalyzed hydrosilylation of alkynes

Absolute transition rates for rare events from dynamical decoupling of reaction variables

Advillin folding takes place on a hypersurface of small dimensionality

Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations.

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling

Anisotropy of Earth's D″ layer and stacking faults in the MgSiO3 post-perovskite phase

Are structural biases at protein termini a signature of vectorial folding?

Assessing the Accuracy of Metadynamics†

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids

Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching.

Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories

Calculating thermodynamics properties of quantum systems by a non-Markovian Monte Carlo procedure

Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

Charge Localization in DNA Fibers

Computational design of cyclic peptides for the customized oriented immobilization of globular proteins

Computing the Free Energy without Collective Variables

Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations.

Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study

Correlations among hydrogen bonds in liquid water

Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions

Deciphering the folding kinetics of transmembrane helical proteins

Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.

Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach.

Dissociation mechanism of acetic acid in water

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

Equilibrium Free Energies from Nonequilibrium Metadynamics

Escaping free-energy minima

Estimating the intrinsic dimension of datasets by a minimal neighborhood information.

Explicit Characterization of the Free-Energy Landscape of a Protein in the Space of All Its Cα Carbons

Exploring the universe of protein structures beyond the Protein Data Bank

Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer

Flexible docking in solution using metadynamics

Force generation in lamellipodia is a probabilistic process with fast growth and retraction events.

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics

Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide

Influence of DNA structure on the reactivity of the guanine radical cation

Initial stages of salt crystal dissolution determined with ab initio molecular dynamics

Machine learning. Clustering by fast search and find of density peaks.

Markov state modeling of sliding friction. ⬇️

Metadynamics convergence law in a multidimensional system

Metadynamics simulations reveal a Na+ independent exiting path of galactose for the inward-facing conformation of vSGLT

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

Microscopic Mechanism of Antibiotics Translocation through a Porin

Multidimensional view of amyloid fibril nucleation in atomistic detail.

Native fold and docking pose discrimination by the same residue-based scoring function.

New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods.

Non-Markovian effects on protein sequence evolution due to site dependent substitution rates

Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model.

Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment

Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations

Physics of iron at Earth's core conditions

Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms

Predicting Crystal Structures: The Parrinello-Rahman Method Revisited

Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations

Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants.

Preface: Special Topic on Enhanced Sampling for Molecular Systems

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4.

Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

Shape and area fluctuation effects on nucleation theory ⬇️