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List of works by Raffaello Potestio

A deep learning approach to the structural analysis of proteins

scientific article published on 19 April 2019

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

scientific article published on 3 October 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.

scientific article published on 5 May 2010

Adaptive Resolution Simulations with Self-Adjusting High-Resolution Regions

scientific article published on 6 July 2016

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

scientific article

Adaptive resolution simulation of oligonucleotides

scientific article published in December 2016

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

scientific article published on 27 October 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

scientific article published in October 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

scientific article published on 23 May 2018

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

scientific article (publication date: 2012)

Discretized knot motion on a tensioned fiber induced by transverse waves

scientific article published on 29 October 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)].

scientific article published in January 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

scientific article

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

scientific article published in December 2017

Hamiltonian adaptive resolution simulation for molecular liquids.

scientific article published on 5 March 2013

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

scientific article published in 2022

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

scientific article

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

scientific article published on 11 June 2020

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

scientific article (publication date: 2013)

Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids

scientific article published in Physical Review Letters

Nuclear Quantum Effects in Water: A Multiscale Study

scientific article published on 23 January 2014

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

scientific article

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

scientific article published on 28 February 2019

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

scientific article published on 14 December 2018

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

scientific article

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

scientific article published on 7 February 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

scientific article published on 22 September 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

scientific article published on 20 June 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

scientific article published on 01 October 2019

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

scientific article published on 04 November 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

scientific article published on 22 June 2016

Two Adhesive Sites Can Enhance the Knotting Probability of DNA.

scientific article published on 2 July 2015

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

scientific article published in June 2017

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