Lista de obras - Alessandro Laio - Dominio Público Uruguay

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

artículo científico publicado en 2013

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

artículo científico publicado en 2009

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

artículo científico publicado en 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

artículo científico publicado en 2006

A Variational Definition of Electrostatic Potential Derived Charges

A comparative theoretical study of dipeptide solvation in water.

artículo científico publicado en 2006

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

artículo científico publicado en 2013

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

artículo científico publicado en 2009

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

artículo científico publicado en 2004

A molecular spring for vision.

artículo científico publicado en 2004

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

artículo científico publicado en 2005

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

artículo científico publicado en 2015

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

artículo científico publicado en 2005

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

artículo científico publicado en 2012

Advillin folding takes place on a hypersurface of small dimensionality

artículo científico publicado en 2008

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

artículo científico publicado en 2015

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

artículo científico publicado en 2006

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling

artículo científico publicado en 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?

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 2007

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

artículo científico publicado en 2004

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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2011

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

artículo científico publicado en 2008

Correlations among hydrogen bonds in liquid water

artículo científico publicado en 2004

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

artículo científico publicado en 2011

Deciphering the folding kinetics of transmembrane helical proteins

artículo científico publicado en 2000

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

artículo científico publicado en 2015

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

artículo científico publicado en 2012

Dissociation mechanism of acetic acid in water

artículo científico publicado en 2006

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

artículo científico publicado en 2003

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

artículo científico publicado en 2006

Equilibrium Free Energies from Nonequilibrium Metadynamics

artículo científico publicado en 2006

Escaping free-energy minima

artículo científico publicado en 2002

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2005

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

artículo científico publicado en 2010

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

artículo científico publicado en 2006

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

artículo científico publicado en 2016

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

artículo científico publicado en 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.

artículo científico publicado en 2014

Markov state modeling of sliding friction. ⬇️

artículo científico publicado en 2016

Metadynamics convergence law in a multidimensional system

artículo científico publicado en 2010

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

artículo científico publicado en 2014

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

artículo científico publicado en 2004

Multidimensional view of amyloid fibril nucleation in atomistic detail.

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

artículo científico publicado en 2017

Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations

artículo científico publicado en 2016

Physics of iron at Earth's core conditions

artículo científico publicado en 2000

Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms

artículo científico publicado en 2017

Predicting Crystal Structures: The Parrinello-Rahman Method Revisited

artículo científico publicado en 2003

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.

artículo científico publicado en 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.

artículo científico publicado en 2016

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

artículo científico publicado en 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.

artículo científico publicado en 2016

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

artículo científico publicado en 2016

Shape and area fluctuation effects on nucleation theory ⬇️

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2009

The intrinsic dimension of protein sequence evolution

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

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado en 2009

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

artículo científico publicado en 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.

artículo científico publicado en 2016

Lista de obras de 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 ⬇️