Lista de obras - Raffaello Potestio - Dominio Público Uruguay

A deep learning approach to the structural analysis of proteins

artículo científico publicado en 2019

A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site ⬇️

artículo científico publicado en 2016

A unified framework for force-based and energy-based adaptive resolution simulations

ALADYN: a web server for aligning proteins by matching their large-scale motion.

artículo científico publicado en 2010

Adaptive Resolution Simulations with Self-Adjusting High-Resolution Regions

artículo científico publicado en 2016

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties.

artículo científico publicado en 2015

Adaptive resolution simulation of oligonucleotides

artículo científico publicado en 2016

An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules

artículo científico publicado en 2020

Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles

Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations

artículo científico publicado en 2016

Computational methods in the study of self-entangled proteins: a critical appraisal

scientific article published on 03 July 2019

Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations

artículo científico publicado en 2018

Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations

artículo científico publicado en 2012

Discretized knot motion on a tensioned fiber induced by transverse waves

artículo científico publicado en 2015

Envisioning data sharing for the biocomputing community

scientific article published on 19 April 2019

Erratum: "Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties" [J. Chem. Phys. 142, 195101 (2015)].

artículo científico publicado en 2017

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations

scholarly article by M. Heidari published in June 2018

Folding of small knotted proteins: Insights from a mean field coarse-grained model

article

From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations

artículo científico publicado en 2016

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

artículo científico publicado en 2017

Hamiltonian adaptive resolution simulation for molecular liquids.

artículo científico publicado en 2013

In Search of a Dynamical Vocabulary: A Pipeline to Construct a Basis of Shared Traits in Large-Scale Motions of Proteins

artículo científico publicado en 2022

Knotted vs. unknotted proteins: evidence of knot-promoting loops

artículo científico publicado en 2010

Ligand-protein interactions in lysozyme investigated through a dual-resolution model

artículo científico publicado en 2020

Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition

artículo científico publicado en 2013

Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids

artículo científico publicado en 2013

Nuclear Quantum Effects in Water: A Multiscale Study

artículo científico publicado en 2014

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

artículo científico publicado en 2017

Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes

artículo científico publicado en 2019

Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules

artículo científico publicado en 2018

PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains

artículo científico publicado en 2009

Quantum locality and equilibrium properties in low-temperature parahydrogen: A multiscale simulation study

artículo científico publicado en 2012

Random Matrix Approach to Collective Behavior and Bulk Universality in Protein Dynamics

scientific article published in Physical Review Letters

Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers

artículo científico publicado en 2016

Searching the Optimal Folding Routes of a Complex Lasso Protein

scientific article published on 07 June 2019

Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids

artículo científico publicado en 2018

Statistical mechanics of Hamiltonian adaptive resolution simulations ⬇️

scientific article published on 01 February 2015

Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences

artículo científico publicado en 2019

Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental-Computational Approach

artículo científico publicado en 2019

The relative entropy is fundamental to adaptive resolution simulations

scientific article published on 01 July 2016

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

artículo científico publicado en 2016

Two Adhesive Sites Can Enhance the Knotting Probability of DNA.

artículo científico publicado en 2015

Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues

artículo científico publicado en 2017

Lista de obras de Raffaello Potestio

A deep learning approach to the structural analysis of proteins

A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site ⬇️

A unified framework for force-based and energy-based adaptive resolution simulations

ALADYN: a web server for aligning proteins by matching their large-scale motion.

Adaptive Resolution Simulations with Self-Adjusting High-Resolution Regions

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties.

Adaptive resolution simulation of oligonucleotides

An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules

Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles

Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations

Computational methods in the study of self-entangled proteins: a critical appraisal

Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations

Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations

Discretized knot motion on a tensioned fiber induced by transverse waves

Envisioning data sharing for the biocomputing community

Erratum: "Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties" [J. Chem. Phys. 142, 195101 (2015)].

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations

Folding of small knotted proteins: Insights from a mean field coarse-grained model

From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations

From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics

Hamiltonian adaptive resolution simulation for molecular liquids.

In Search of a Dynamical Vocabulary: A Pipeline to Construct a Basis of Shared Traits in Large-Scale Motions of Proteins

Knotted vs. unknotted proteins: evidence of knot-promoting loops

Ligand-protein interactions in lysozyme investigated through a dual-resolution model

Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition

Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids

Nuclear Quantum Effects in Water: A Multiscale Study

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes

Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules

PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains

Quantum locality and equilibrium properties in low-temperature parahydrogen: A multiscale simulation study

Random Matrix Approach to Collective Behavior and Bulk Universality in Protein Dynamics

Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers

Searching the Optimal Folding Routes of a Complex Lasso Protein

Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids

Statistical mechanics of Hamiltonian adaptive resolution simulations ⬇️

Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences

Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental-Computational Approach

The relative entropy is fundamental to adaptive resolution simulations

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials

Two Adhesive Sites Can Enhance the Knotting Probability of DNA.

Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues