Lista de obras - Piero Procacci - Dominio Público Uruguay

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

artículo científico publicado en 2009

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

artículo científico publicado en 2019

An ab initio force field for the cofactors of bacterial photosynthesis

artículo científico publicado en 2003

Anharmonic lattice dynamics and computer simulation for simple model systems

artículo científico publicado en 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

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2017

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2001

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

artículo científico publicado en 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

artículo científico publicado en 2011

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

artículo científico publicado en 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.

artículo científico publicado en 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

artículo científico publicado en 1993

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2019

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

artículo científico publicado en 2014

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

artículo científico publicado en 2009

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

artículo científico publicado en 2010

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

artículo científico publicado en 2007

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2004

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

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2007

Lipid tempering simulation of model biological membranes on parallel platforms

artículo científico publicado en 2018

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

artículo científico publicado en 2006

Multiple Bennett acceptance ratio made easy for replica exchange simulations

artículo científico publicado en 2013

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

artículo científico publicado en 2018

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

artículo científico publicado en 2007

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

artículo científico publicado en 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.

artículo científico publicado en 2017

Reformulating the entropic contribution in molecular docking scoring functions

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 2022

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

artículo científico publicado en 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

artículo científico publicado en 2002

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

artículo científico publicado en 2017

The nature of intermolecular interactions between aromatic amino acid residues

artículo científico publicado en 2002

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

artículo científico publicado en 2013

Thermodynamics of stacking interactions in proteins.

artículo científico publicado en 2008

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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 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

Lista de obras de Piero Procacci

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

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

An ab initio force field for the cofactors of bacterial photosynthesis

Anharmonic lattice dynamics and computer simulation for simple model systems

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Density Functional Calculation of Structural and Vibrational Properties of Glycerol

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

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

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

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

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

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

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

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

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

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

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

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

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

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

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

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

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

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

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

Lipid tempering simulation of model biological membranes on parallel platforms

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

Multiple Bennett acceptance ratio made easy for replica exchange simulations

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

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

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

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

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

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

Reformulating the entropic contribution in molecular docking scoring functions

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

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

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

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

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

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

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

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

The nature of intermolecular interactions between aromatic amino acid residues

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

Thermodynamics of stacking interactions in proteins.

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

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

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

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

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