Alessandro Laio

Q: What Schools Are Affiliated With Alessandro Laio

Alessandro Laio is affiliated with the following schools: Warsaw University of Technology, ETH Zurich, Polytechnic University of Turin, University of Padua, International School for Advanced Studies

Alessandro Laio's AcademicInfluence.com Rankings

Alessandro Laio

Physics

#6388

World Rank

#8328

Historical Rank

Biophysics

#260

World Rank

#271

Historical Rank

physics Degrees

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Physics

Alessandro Laio's Degrees

Masters Physics University of Padua
Bachelors Physics University of Padua

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Alessandro Laio's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Escaping free-energy minima (2002) (4014)
Clustering by fast search and find of density peaks (2014) (2176)
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science (2008) (1251)
Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. (2003) (602)
A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations (2002) (488)
A bias-exchange approach to protein folding. (2007) (473)
Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. (2015) (469)
Predicting crystal structures: the Parrinello-Rahman method revisited. (2002) (461)
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. (2006) (445)
Promoting transparency and reproducibility in enhanced molecular simulations (2019) (437)
Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. (2006) (413)
Assessing the accuracy of metadynamics. (2005) (398)
Equilibrium free energies from nonequilibrium metadynamics. (2006) (340)
A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations (2009) (245)
Flexible docking in solution using metadynamics. (2005) (240)
A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. (2005) (212)
Anisotropy of Earth's D″ layer and stacking faults in the MgSiO3 post-perovskite phase (2005) (210)
An Efficient Real Space Multigrid QM/MM Electrostatic Coupling. (2005) (203)
Using metadynamics to explore complex free-energy landscapes (2020) (195)
Estimating the intrinsic dimension of datasets by a minimal neighborhood information (2017) (190)
The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases. (2007) (175)
D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations (2002) (153)
An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations. (2006) (143)
A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1. (2009) (142)
Intrinsic dimension of data representations in deep neural networks (2019) (136)
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. (2009) (133)
Reconstructing the density of states by history-dependent metadynamics. (2004) (129)
Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics (2013) (125)
Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. (2006) (106)
The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments (2015) (104)
QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water. (2003) (97)
Simulation of structural phase transitions by metadynamics (2004) (96)
Unsupervised Learning Methods for Molecular Simulation Data (2021) (94)
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations (2012) (81)
Dissociation mechanism of acetic acid in water. (2006) (80)
Systematic improvement of classical nucleation theory. (2012) (80)
A molecular spring for vision. (2004) (79)
Metadynamics convergence law in a multidimensional system. (2010) (79)
Multidimensional view of amyloid fibril nucleation in atomistic detail. (2012) (75)
Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching. (2007) (74)
Microscopic Mechanism of Antibiotics Translocation through a Porin. (2004) (73)
Physical origin of selectivity in ionic channels of biological membranes. (1999) (69)
A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion. (2004) (66)
Exploring the Universe of Protein Structures beyond the Protein Data Bank (2010) (66)
Vacancy-vacancy interaction and oxygen diffusion in stabilized cubic ZrO2 from first principles (2008) (65)
Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms. (2004) (62)
“Site Binding” of Ca2+ Ions to Polyacrylates in Water: A Molecular Dynamics Study of Coiling and Aggregation (2007) (58)
Correlations among hydrogen bonds in liquid water. (2004) (56)
Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions (2002) (56)
Atomistic structure of cobalt-phosphate nanoparticles for catalytic water oxidation. (2012) (54)
Influence of DNA structure on the reactivity of the guanine radical cation. (2004) (54)
A novel approach to the investigation of passive molecular permeation through lipid bilayers from atomistic simulations. (2012) (51)
Initial stages of salt crystal dissolution determined with ab initio molecular dynamics. (2011) (50)
Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations (2012) (49)
Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants. (2008) (49)
Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions (2011) (48)
A simple and efficient statistical potential for scoring ensembles of protein structures (2012) (48)
Nucleation process of a fibril precursor in the C-terminal segment of amyloid-β. (2013) (43)
Charge localization in DNA fibers. (2005) (42)
Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model. (2010) (41)
Computing Free Energies and Accelerating Rare Events with Metadynamics (2006) (40)
Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations. (2008) (40)
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. (2016) (38)
The energy gap as a universal reaction coordinate for the simulation of chemical reactions. (2009) (37)
Characterization of the Dizinc Analogue of the Synthetic Diiron Protein DF1 Using ab Initio and Hybrid Quantum/Classical Molecular Dynamics Simulations (2003) (35)
Computing the Free Energy without Collective Variables. (2018) (34)
Metadynamics surfing on topology barriers: the CPN−1 case (2015) (31)
Shape and area fluctuation effects on nucleation theory. (2014) (30)
A comparative theoretical study of dipeptide solvation in water (2006) (29)
METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations (2017) (29)
Force generation in lamellipodia is a probabilistic process with fast growth and retraction events. (2010) (29)
Automatic topography of high-dimensional data sets by non-parametric Density Peak clustering (2018) (28)
A variational definition of electrostatic potential derived charges (2004) (28)
Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory? (2011) (27)
Free Energy ab Initio Metadynamics: A New Tool for the Theoretical Study of Organometallic Reactivity? Example of the C−C and C−H Reductive Eliminations from Platinum(IV) Complexes (2007) (27)
A fingerprint of surface-tension anisotropy in the free-energy cost of nucleation. (2013) (27)
A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations. (2013) (26)
A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels (2015) (26)
Conformations of the Huntingtin N‐term in aqueous solution from atomistic simulations (2011) (25)
Advillin folding takes place on a hypersurface of small dimensionality. (2008) (25)
A consensus protocol for the in silico optimisation of antibody fragments. (2019) (25)
A VMD interface for analyzing metadynamics and molecular dynamics simulations ✩ (2011) (25)
Molecular dynamics simulation of reconstructive phase transitions on an anhydrous zeolite (2004) (25)
Binding affinity prediction of nanobody-protein complexes by scoring of molecular dynamics trajectories. (2018) (24)
Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT (2014) (22)
Dynamical landscape and multistability of a climate model (2020) (20)
Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations (2019) (19)
The Subtle Trade-Off between Evolutionary and Energetic Constraints in Protein-Protein Interactions. (2019) (18)
Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics (2020) (18)
A simple and efficient statistical potential for scoring ensembles of protein (2012) (18)
Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach. (2012) (18)
Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations. (2016) (17)
Are structural biases at protein termini a signature of vectorial folding? (2005) (17)
Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations (2020) (17)
Spontaneously Forming Dendritic Voids in Liquid Water Can Host Small Polymers. (2019) (17)
Peptide biosensors for anticancer drugs: Design in silico to work in denaturizing environment. (2018) (17)
Brain network dynamics during spontaneous strategy shifts and incremental task optimization (2018) (16)
BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures (2013) (16)
Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids. (2018) (16)
Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics. (2015) (15)
Copper binding sites in the C‐terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study (2008) (15)
Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost. (2016) (15)
The intrinsic dimension of protein sequence evolution (2019) (14)
Data segmentation based on the local intrinsic dimension (2019) (14)
Computational design of cyclic peptides for the customized oriented immobilization of globular proteins. (2017) (13)
Native fold and docking pose discrimination by the same residue‐based scoring function (2015) (13)
Tracing the Entropy along a Reactive Pathway: The Energy As a Generalized Reaction Coordinate. (2009) (13)
Ab initio simulations of Lewis-acid-catalyzed hydrosilylation of alkynes. (2005) (12)
An explicit characterization of the free energy landscape of a protein in the space of all its Cα carbons. (2019) (11)
Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer. (2011) (10)
Deciphering the folding kinetics of transmembrane helical proteins. (2000) (10)
Absolute transition rates for rare events from dynamical decoupling of reaction variables. (2012) (10)
Anisotropy of Earth ’ s D ” layer and stacking faults in MgSiO 3 post-perovskite (2009) (10)
Hierarchical nucleation in deep neural networks (2020) (10)
A QUICKSTEP-based quantum mechanics/molecular mechanics approach for silica. (2006) (10)
Protein–protein structure prediction by scoring molecular dynamics trajectories of putative poses (2016) (9)
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates (2016) (9)
Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide (2016) (9)
In Silico Design of Short Peptides as Sensing Elements for Phenolic Compounds (2016) (9)
Hybrid QM/MM Car—Parrinello Simulations of Catalytic and Enzymatic Reactions (2010) (9)
QUANTUM THEORY OF FREQUENCY SHIFTS OF AN ELECTROMAGNETIC WAVE INTERACTING WITH A PLASMA (1997) (7)
New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods (2017) (7)
PARCE: Protocol for Amino acid Refinement through Computational Evolution (2020) (7)
Ranking the information content of distance measures (2021) (7)
DADApy: Distance-based analysis of data-manifolds in Python (2022) (7)
fMRI single trial discovery of spatio‐temporal brain activity patterns (2017) (6)
Calculating thermodynamics properties of quantum systems by a non-Markovian Monte Carlo procedure. (2009) (6)
Theory of the reentrant quantum rotational phase transition in high-pressure HD (2011) (6)
A third hypothesis on the origin of the redshift: application to the Pioneer-6 data (1995) (6)
QMMMW: A wrapper for QM/MM simulations with Quantum ESPRESSO and LAMMPS (2015) (5)
Markov state modeling of sliding friction. (2016) (5)
Model Folded Hydrophobic Polymers Reside in Highly Branched Voids. (2021) (4)
Clustering by the local intrinsic dimension: the hidden structure of real-world data (2019) (4)
Preface: Special Topic on Enhanced Sampling for Molecular Systems. (2018) (4)
A Rosetta-based protein design protocol converging to natural sequences. (2021) (4)
Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol (2022) (4)
Monte Carlo approach to the conformal bootstrap (2022) (4)
Distributional Results for Model-Based Intrinsic Dimension Estimators (2021) (4)
Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples (2020) (3)
A common root for coevolution and substitution rate variability in protein sequence evolution (2019) (3)
Computational Evolution Protocol for Peptide Design. (2022) (3)
Statistically unbiased free energy estimates from biased simulations (2021) (3)
Dynamical Landscape and Multistability of the Earth's Climate (2020) (3)
Vibrational entropy estimation can improve binding affinity prediction for non‐obligatory protein complexes (2018) (3)
Simulation of Amyloid Nucleation with Bias-Exchange Metadynamics (2012) (2)
Toward a unified scoring function for native state discrimination and drug-binding pocket recognition. (2018) (2)
Prune and distill: similar reformatting of image information along rat visual cortex and deep neural networks (2022) (2)
The generalized ratios intrinsic dimension estimator (2022) (2)
Metadynamics Remedies for Topological Freezing (2017) (2)
Thermodynamics of an Intrinsically Disordered Protein by Atomistic Simulations (2013) (2)
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation (2021) (2)
ELECTRON TRANSFER INDUCED DISSOCIATION OF CHLORO-CYANO-BENZENE RADICAL ANION: DRIVING CHEMICAL REACTIONS VIA CHARGE RESTRAINTS (2005) (2)
A Markov state modeling analysis of sliding dynamics of a 2D model. (2017) (1)
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms (2017) (1)
Interacting hard-core bosons and surface preroughening (1998) (1)
DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets (2022) (1)
Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Meta- dynamics Simulations (2011) (1)
Unfolding and identification of membrane proteins from native cell membranes (2019) (1)
Advanced sampling techniques for numerical simulations : lecture notes (2009) (1)
Intrinsic dimension estimation for discrete metrics (2022) (1)
The permeation mechanism of organic cations through a CNG mimic channel (2018) (1)
12 78 4 v 1 [ cs . L G ] 2 9 M ay 2 01 9 Intrinsic dimension of data representations in deep neural networks (2019) (0)
Unfolding and identification of membrane proteins in situ (2019) (0)
Protein Folding by Bias Exchange Metadynamics on a Grid Infrastructure (2009) (0)
Reconstructing the topography of multidimensional probability landscapes E (2018) (0)
Exploring by Enhanced Sampling Techniques: The Protein’s Conformational Space Beyond the PDB (2011) (0)
Metadynamics for transition paths in irreversible dynamics (2022) (0)
First report on verification and validation of codes and on the data analytics pilots (2020) (0)
Quantum frequency shift in an elecromagnetic wave interacting with a plasma (1997) (0)
Clustering and Identification of Force Spectra from Native Membranes (2019) (0)
Mechanism of Ionic Permeation in the Mimics of CNG Channels: A Structural, Functional and Computational Analysis (2014) (0)
Translocation mechanism of ions in channels and enzymatic gorges (2005) (0)
Supporting Information : Initial stages of salt crystal dissolution determined with ab initio molecular dynamics (2011) (0)
The geometry of hidden representations of large transformer models (2023) (0)
Computational Design of Peptides Bound to the Major Histocompatibility Complex Class II (2020) (0)
Estimating the intrinsic dimension of datasets by a minimal neighborhood information (2017) (0)
Ab initio molecular dynamics study of the E2 and Sn2 reaction between X-+CH3CH2Y (2003) (0)
Redundant representations help generalization in wide neural networks (2021) (0)
Optimal inference of a generalised Potts model by single-layer transformers with factored attention (2023) (0)
COMP 463-Free-energy landscapes from combined parallel-tempering and metadynamics (2007) (0)
Step–step interactions and correlations from 1D hard-core boson mapping (1998) (0)
Bayesian dimensionality reduction via identifications of data intrinsic dimensions (2019) (0)
DPCfam: a new method for unsupervised protein family classification (2020) (0)
Atomistic Simulations of Short Peptides Aggregation by Advanced Computational Techniques (2012) (0)
Modelling the impact of financialization on agricultural commodity markets (2016) (0)
Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations (2009) (0)
QM/MM Simulation of the First Step of Vision (2005) (0)
PHYS 410-Beta-hairpin folding with parallel-tempering and metadynamics (2007) (0)
Using metadynamics to explore complex free-energy landscapes (2020) (0)
Atomistic Prediction of the structure of the Advillin headpiece and its Pro62Ala mutant (2007) (0)
Sodium-Galactose Transporter: The First Steps of the Transport Mechanism Investigated by Molecular Dynamics (2014) (0)
Optimal transfer protocol by incremental layer defrosting (2023) (0)
New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods (2017) (0)
Atomistic Study of Structural and Functional Properties of Membrane Proteins (2014) (0)
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates (2016) (0)
Mechanism of oxidative damage to DNA (2003) (0)
Simulation of Iron at Earth's Core Conditions (2007) (0)
Improving acute stroke assessment in non-enhanced CT: Automated tool for early ischemic lesion volume detection (2021) (0)
Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water. (2022) (0)
Atomistic Simulation Studies of the Permeation of Organic Molecules Through Lipid Membranes (2012) (0)
Mechanical interactions may explain synchronized growth of cytoskeletal actin networks in motile cells (2012) (0)
Novel high-pressure phases: theory and experiment (2005) (0)
Detection and Characterization of elementary events underlying force generation in lamellipodia of Dorsal Root Ganglia Neurons (2009) (0)
Representation mitosis in wide neural networks (2021) (0)
When kinetics plays strange tricks (2022) (0)
Interacting hard-core bosons and surface physics (1997) (0)
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation (2021) (0)
Cover Picture: QM/MM Car‐Parrinello Molecular Dynamics Study of the Solvent Effects on the Ground State and on the First Excited Singlet State of Acetone in Water (ChemPhysChem 11/2003) (2003) (0)
Computational design of high-affinity peptides bound to the Major Histocompatibility Complex class II (2020) (0)

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What Schools Are Affiliated With Alessandro Laio?

Alessandro Laio is affiliated with the following schools: