Alessandro Laio

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Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT

Ina Bisha, Alex Rodriguez, Alessandro Laio, 2014, PLoS Comput. Biol..

BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures

Alessandro Laio, E. Sarti, S. Zamuner, 2013, Comput. Phys. Commun..

The intrinsic dimension of protein sequence evolution

Alessandro Laio, Elena Facco, Andrea Pagnani, 2019, PLoS Comput. Biol..

PARCE: Protocol for Amino acid Refinement through Computational Evolution

Alessandro Laio, Pilar Cossio, Rodrigo Ochoa, 2020, Comput. Phys. Commun..

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Alessandro Laio, Fabio Pietrucci, Xevi Biarnés, 2012, Comput. Phys. Commun..

Exploring the Universe of Protein Structures beyond the Protein Data Bank

Alessandro Laio, Fabio Pietrucci, Pilar Cossio, 2010, PLoS Comput. Biol..

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

Alessandro Laio, Flavio Seno, Antonio Trovato, 2015, Proteins.

Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples

Alessandro Laio, Marco Brucale, Nina I Ilieva, 2020, Bioinform..

Data segmentation based on the local intrinsic dimension

Alessandro Laio, Elena Facco, Antonietta Mira, 2020, Scientific reports.

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

Alessandro Laio, Stefano Zamuner, Edoardo Sarti, 2018, Physical chemistry chemical physics : PCCP.

A simple and efficient statistical potential for scoring ensembles of protein structures

Alessandro Laio, Pilar Cossio, Flavio Seno, 2012, Scientific Reports.

QMMMW: A wrapper for QM/MM simulations with Quantum ESPRESSO and LAMMPS

Alessandro Laio, Layla Martin-Samos, Changru Ma, 2015, Comput. Phys. Commun..

Computational Design of Peptides Bound to the Major Histocompatibility Complex Class II

Alessandro Laio, Rodrigo Ochoa, Pilar Cossio, 2020 .

Predicting the affinity of peptides to MHC class II by scoring molecular dynamics simulations.

Alessandro Laio, Rodrigo Ochoa, Pilar Cossio, 2019, Journal of chemical information and modeling.

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

Alessandro Laio, Anne Milet, Carine Michel, 2009, Journal of chemical theory and computation.

A simple and efficient statistical potential for scoring ensembles of protein

Alessandro Laio, Flavio Seno, Antonio Trovato, 2012 .

A consensus protocol for the in silico optimisation of antibody fragments.

Alessandro Laio, Paola Storici, Miguel A. Soler, 2019, Chemical communications.

Preface: Special Topic on Enhanced Sampling for Molecular Systems.

Alessandro Laio, Daniel M Zuckerman, Athanassios Z Panagiotopoulos, 2018, The Journal of chemical physics.

A comparative theoretical study of dipeptide solvation in water

Alessandro Laio, Ursula Rothlisberger, Patrick Maurer, 2006, J. Comput. Chem..

Clustering by the local intrinsic dimension: the hidden structure of real-world data pdf

Alessandro Laio, Elena Facco, Antonietta Mira, 2019, ArXiv.

Using metadynamics to explore complex free-energy landscapes

Alessandro Laio, Giovanni Bussi, A. Laio, 2020 .

METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations

Alex Rodriguez, Alessandro Laio, Toni Giorgino, 2017, Comput. Phys. Commun..

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Alessandro Laio, Fabio Pietrucci, Stefano Piana, 2009, PLoS Comput. Biol..

Automatic topography of high-dimensional data sets by non-parametric Density Peak clustering pdf

Alex Rodriguez, Alessandro Laio, Elena Facco, 2018, Inf. Sci..

Clustering by fast search and find of density peaks

Alessandro Laio, Alex Rodriguez, Alex Rodriguez, 2014, Science.

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

Alex Rodriguez, Alessandro Laio, Francesca Rizzato, 2016, BMC Bioinformatics.

The permeation mechanism of organic cations through a CNG mimic channel

Alessandro Laio, Alex Rodriguez, Vincent Torre, 2018, PLoS Comput. Biol..

Reconstructing the topography of multidimensional probability landscapes E

Alex Rodriguez, Alessandro Laio, Elena Facco, 2018 .

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

Alessandro Laio, Fabio Pietrucci, A. Laio, 2009, Journal of chemical theory and computation.

DPCfam: a new method for unsupervised protein family classification

Alessandro Laio, Elena Tea Russo, Marco Punta, 2020 .

Hierarchical nucleation in deep neural networks pdf

Alessandro Laio, Alessio Ansuini, Aldo Glielmo, 2020, NeurIPS.

Estimating the intrinsic dimension of datasets by a minimal neighborhood information

Alessandro Laio, Elena Facco, Maria d'Errico, 2017, Scientific Reports.

Intrinsic dimension of data representations in deep neural networks

Alessandro Laio, Jakob H. Macke, Davide Zoccolan, 2019, NeurIPS.

Brain network dynamics during spontaneous strategy shifts and incremental task optimization

Alessandro Laio, Carlo Reverberi, Nicolas W. Schuck, 2018, NeuroImage.

Statistically unbiased free energy estimates from biased simulations

Alessandro Laio, Matteo Carli, A. Laio, 2021, Molecular Physics.

Representation mitosis in wide neural networks pdf

Alessandro Laio, Aldo Glielmo, Diego Doimo, 2021, ArXiv.

Dynamical landscape and multistability of a climate model

Alessandro Laio, Valerio Lucarini, Tobias Grafke, 2021, Proceedings of the Royal Society A.

Ranking the information content of distance measures pdf

Alessandro Laio, Gabor Csanyi, Aldo Glielmo, 2021, ArXiv.

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation

Alessandro Laio, Marco Punta, Elena Tea Russo, 2021, BMC Bioinformatics.

Distributional Results for Model-Based Intrinsic Dimension Estimators

Alessandro Laio, Antonietta Mira, Francesco Denti, 2021 .

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

Alessandro Laio, Francesco Difato, Enrico Ferrari, 2010, Biophysical journal.

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

Alessandro Laio, Alex Rodriguez, Federico Berti, 2015, The journal of physical chemistry. B.

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

Alessandro Laio, Giuseppe Toffoli, Anna Battisti, 2018, Biosensors & bioelectronics.

Reconstructing the density of states by history-dependent metadynamics.

Alessandro Laio, Michele Parrinello, Cristian Micheletti, 2004, Physical review letters.

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

Alessandro Laio, Erio Tosatti, A. Laio, 2011, Journal of the American Chemical Society.

Alessandro Laio, Fabio Pietrucci, Pilar Cossio, 2011, Physical chemistry chemical physics : PCCP.

Microscopic Mechanism of Antibiotics Translocation through a Porin.

Alessandro Laio, Michele Parrinello, Christophe Danelon, 2004, Biophysical journal.

A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations

Alessandro Laio, Joost VandeVondele, Ursula Rothlisberger, 2002 .

Advillin folding takes place on a hypersurface of small dimensionality.

Alessandro Laio, Stefano Piana, 2008, Physical review letters.

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling.

Alessandro Laio, Fawzi Mohamed, Michele Parrinello, 2005, Journal of chemical theory and computation.

Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer.

Alessandro Laio, Michele Parrinello, Nazario Tantalo, 2006, Biophysical journal.

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

Alessandro Laio, Francesco Luigi Gervasio, Marcella Iannuzzi, 2004, Chemistry.

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

Alessandro Laio, Fawzi Mohamed, Matthias Krack, 2007 .

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

Alessandro Laio, Michele Parrinello, Bernd Ensing, 2005, The journal of physical chemistry. B.

A third hypothesis on the origin of the redshift: application to the Pioneer-6 data

Alessandro Laio, Luigi Accardi, G. Rizzi, 1995 .

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

Alessandro Laio, Marcella Iannuzzi, Michele Parrinello, 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

Alessandro Laio, Giorgio Colombo, Riccardo Capelli, 2019, The journal of physical chemistry letters.

Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations

Alessandro Laio, Fabio Pietrucci, Pilar Cossio, 2012 .

Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations.

Alessandro Laio, Giovanni Bussi, Cristian Micheletti, 2008, The Journal of chemical physics.

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

Alessandro Laio, Francesco L Gervasio, Michele Parrinello, 2004, Journal of the American Chemical Society.

“Site Binding” of Ca2+ Ions to Polyacrylates in Water: A Molecular Dynamics Study of Coiling and Aggregation

Alessandro Laio, Michele Parrinello, Ferenc Molnar, 2007 .

A VMD interface for analyzing metadynamics and molecular dynamics simulations ✩

Alessandro Laio, Fabio Pietrucci, Fabrizio Marinelli, 2011 .

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

Alessandro Laio, Artem R. Oganov, Michele Parrinello, 2005, Nature.

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

Alessandro Laio, Petr Kulhánek, István Simon, 2009, The journal of physical chemistry. B.

Multidimensional view of amyloid fibril nucleation in atomistic detail.

Alessandro Laio, Fabio Pietrucci, Fabio Affinito, 2012, Journal of the American Chemical Society.

Metadynamics convergence law in a multidimensional system.

Alessandro Laio, Fabio Pietrucci, Fabrizio Marinelli, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

Alessandro Laio, Michele Parrinello, A. Laio, 2007, Journal of the American Chemical Society.

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

Alessandro Laio, Fawzi Mohamed, Michele Parrinello, 2006, Journal of chemical theory and computation.

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

Alessandro Laio, Michele Parrinello, Teodoro Laino, 2006, The Journal of chemical physics.

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

Alessandro Laio, Ursula Rothlisberger, A. Laio, 2007, Journal of chemical theory and computation.

Metadynamics surfing on topology barriers: the CPN−1 case

Alessandro Laio, Francesco Sanfilippo, A. Laio, 2015, 1508.07270.

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

Alessandro Laio, Marcella Iannuzzi, Michele Parrinello, 2003, Physical review letters.

Vacancy-vacancy interaction and oxygen diffusion in stabilized cubic ZrO2 from first principles

Alessandro Laio, Fabio Pietrucci, Michele Parrinello, 2008 .

In Silico Design of Short Peptides as Sensing Elements for Phenolic Compounds

Alessandro Laio, Dario Compagnone, Michele Del Carlo, 2016 .

Dissociation mechanism of acetic acid in water.

Alessandro Laio, Marcella Iannuzzi, Michele Parrinello, 2006, Journal of the American Chemical Society.

A molecular spring for vision.

Alessandro Laio, Ursula Rothlisberger, Leonardo Guidoni, 2004, Journal of the American Chemical Society.

Computing the Free Energy without Collective Variables.

Alessandro Laio, Elena Facco, Alex Rodriguez, 2018, Journal of chemical theory and computation.

D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations

Alessandro Laio, Joost VandeVondele, Ursula Rothlisberger, 2002 .