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List of works by Piero Procacci

A potential of mean force estimator based on nonequilibrium work exponential averages.

scientific article published on 8 January 2009

Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches

scientific article published on 01 October 2019

An ab initio force field for the cofactors of bacterial photosynthesis

scientific article published on 01 January 2003

Anharmonic lattice dynamics and computer simulation for simple model systems

scientific article published on 01 February 1992

Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules

scientific article published on 14 February 2019

Behavior of polarizable models in presence of strong electric fields. I. Origin of nonlinear effects in water point-charge systems

scientific article published on 01 November 2005

Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation.

scientific article published on 7 November 2017

Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework

scientific article

Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators

scientific article published on 04 March 2008

Chemical-physical analysis of a tartrate model compound for TACE inhibition.

scientific article published in November 2013

Chiral/ring closed vs. achiral/open chain triazine-based organogelators: induction and amplification of supramolecular chirality in organic gels.

scientific article

Comment on "Efficient stress relaxation in molecular dynamics simulations of semiflexible n-alkanes"

scientific article published on 23 January 2001

Comment on "Statistical efficiency of methods for computing free energy of hydration" [J. Chem. Phys. 149, 144111 (2018)]

scientific article published on 01 March 2019

Comment on "from subtle to substantial: role of metal ions on pi-pi interactions"

scientific article published on 01 May 2006

Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases

scientific article published on 01 June 2005

Conformational Landscape of N-Glycosylated Peptides Detecting Autoantibodies in Multiple Sclerosis, Revealed by Hamiltonian Replica Exchange

scientific article published on 30 April 2012

Conformational structure of the MOG-derived peptide 101-108 in solution

scientific article published on 01 January 2011

Correction to "Free Energy Reconstruction in Bidirectional Force Spectroscopy Experiments: The Effect of the Device Stiffness".

scientific article published on 7 July 2016

Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states

scientific article published on 01 August 2018

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.

scientific article published in October 2006

Density Functional Calculation of Structural and Vibrational Properties of Glycerol

article

Determination of the Potential of Mean Force of Aromatic Amino Acid Complexes in Various Solvents Using Molecular Dynamics Simulations: The Case of the Tryptophan−Histidine Pair

article

Efficient calculation of high-order self-energy corrections to phonon linewidths: Application to alpha -nitrogen

scientific article published on 01 May 1993

Efficient nonequilibrium method for binding free energy calculations in molecular dynamics simulations

scientific article published in February 2015

Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations

scientific article published in January 2014

Evidence of a Low-High Density Turning Point in Liquid Water at Ordinary Temperature under Pressure: A Molecular Dynamics Study

scientific article published on 08 October 2019

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

scientific article published in July 2014

Fragment 101-108 of myelin oligodendrocyte glycoprotein: a possible lead compound for multiple sclerosis

scientific article published on 01 December 2009

Free energy reconstruction in bidirectional force spectroscopy experiments: the effect of the device stiffness

scientific article published on 01 February 2010

Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations.

scientific article published on 7 May 2007

Hummer and Szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations

scientific article published in July 2010

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations

scientific article published on 27 May 2016

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework. ⬇️

scientific article published on 19 May 2016

II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands.

scientific article published on 19 May 2016

Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration

scientific article published on 30 April 2019

Inter-residue and solvent-residue interactions in proteins: a statistical study on experimental structures

scientific article published in April 2004

Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations

scientific article published on 07 July 2020

Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase protein

scientific article published on 18 April 2011

Is the T-Shaped Toluene Dimer a Stable Intermolecular Complex?

Key role of the polarization anisotropy of water in modeling classical polarizable force fields

scientific article published on 01 August 2007

Lipid tempering simulation of model biological membranes on parallel platforms

scientific article published on 01 May 2018

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding

scientific article published in March 2006

Multiple Bennett acceptance ratio made easy for replica exchange simulations

scientific article published in September 2013

Myeloid Cell Leukemia 1 Inhibition: An in Silico Study Using Non-equilibrium Fast Double Annihilation Technology

scientific article published on 20 June 2018

Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations.

scientific article published in July 2007

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

scientific article published on 01 April 2010

Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: implications for charge transfer

scientific article published on 01 February 2005

Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates

scientific article published on 01 October 2019

PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules.

scientific article published on 6 June 2017

Reformulating the entropic contribution in molecular docking scoring functions

scientific article published on 27 May 2016

Regioselective electrophilic access to naphtho[1,2-b:8,7-b']- and -[1,2-b:5,6-b']dithiophenes

scientific article published on 11 March 2013

Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach

scientific article published on 01 June 2022

SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches

scientific article published on 17 October 2019

SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

scientific article published on 01 July 2006

Solvation free energies via alchemical simulations: let's get honest about sampling, once more

scientific article published on 18 June 2019

Stacking and T-shape competition in aromatic-aromatic amino acid interactions

scientific article published in May 2002

Statistical Mechanics of Ligand-Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

scientific article published on 7 April 2017

The nature of intermolecular interactions between aromatic amino acid residues

scientific article

The precise chemical-physical nature of the pharmacore in FK506 binding protein inhibition: ElteX, a New class of nanomolar FKBP12 ligands.

scientific article published on 24 January 2013

Thermodynamics of stacking interactions in proteins.

scientific article published on 9 April 2008

Thia-bridged triarylamine heterohelicene radical cations as redox-driven molecular switches

scientific article published on 01 July 2015

Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures.

scientific article published in April 2015

Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins

scientific article published on 16 June 2020

Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands

scientific article published on 21 August 2019

Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease

scientific article published on 22 October 2020

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