P. Procacci

发表

Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm

P. Procacci, M. Marchi, 1996 .

Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems

G. Martyna, P. Procacci, M. Marchi, 1998 .

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

P. Procacci, M. Pagliai, R. Chelli, 2005, The Journal of chemical physics.

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

P. Procacci, R. Chelli, V. Schettino, 2005, The Journal of chemical physics.

A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle

P. Procacci, R. Chelli, 2002 .

Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method

P. Procacci, R. Chelli, G. Cardini, 1999 .

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

F. Gervasio, P. Procacci, R. Chelli, 2002, Journal of the American Chemical Society.

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

P. Procacci, 2015, The Journal of chemical physics.

Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling

P. Procacci, M. Pagliai, Marina Macchiagodena, 2020, Chemical Physics Letters.

MULTIPLE TIME SCALE METHODS FOR CONSTANT PRESSURE MOLECULAR DYNAMICS SIMULATIONS OF MOLECULAR SYSTEMS

B. Berne, P. Procacci, 1994 .

Thermodynamics of stacking interactions in proteins.

Simone Marsili, Riccardo Chelli, Piero Procacci, 2008, Physical chemistry chemical physics : PCCP.

Assessment of GAFF 2 and OPLS-AA general force fields in combination with the water models TIP 3 P , SPCE and OPC 3 for the solvation free energy of drug-like organic molecules

P. Procacci, M. Pagliai, Dario Vassetti, 2019 .

Problems in molecular dynamics of condensed phases

A. Barducci, P. Procacci, M. Pagliai, 2007 .

Misfolding pathways of the prion protein probed by molecular dynamics simulations.

Riccardo Chelli, Piero Procacci, Alessandro Barducci, 2005, Biophysical journal.

Multiple Time Steps Algorithms for the Atomistic Simulations of Complex Molecular Systems

P. Procacci, M. Marchi, 2000 .

Glycerol condensed phases Part I. A molecular dynamics study

Gianni Cardini, Riccardo Chelli, Piero Procacci, 1999 .

Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble

Piero Procacci, Massimo Marchi, P. Procacci, 1998 .

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

P. Procacci, M. Pagliai, R. Chelli, 2017, Journal of chemical theory and computation.

Lipid tempering simulation of model biological membranes on parallel platforms.

A. Barducci, P. Procacci, Chiara Cardelli, 2018, Biochimica et biophysica acta. Biomembranes.

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

P. Procacci, 2019, The Journal of chemical physics.

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

P. Procacci, 2019, The Journal of chemical physics.

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

S. Menichetti, P. Procacci, C. Guardiani, 2015, Journal of chemical theory and computation.

Multiple Bennett acceptance ratio made easy for replica exchange simulations.

P. Procacci, 2013, The Journal of chemical physics.

Mounting evidence of FKBP12 implication in neurodegeneration

P. Procacci, G. Caminati, 2020, Neural regeneration research.

Blocking the FKBP12 induced dendrimeric burst in aberrant aggregation of α-synuclein by using the ElteN378 synthetic inhibitor

S. Menichetti, P. Procacci, M. Martina, 2019, Journal of enzyme inhibition and medicinal chemistry.

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

S. Menichetti, P. Procacci, C. Guardiani, 2013, Physical chemistry chemical physics : PCCP.

SAMPL9 blind predictions using nonequilibrium alchemical approaches.

G. Guarnieri, P. Procacci, 2022, The Journal of chemical physics.

A General Algorithm for Computing Voronoi Volumes - Application to the Hydrated Crystal of Myoglobin

Piero Procacci, Riccardo Scateni, R. Scateni, 1992 .

Thermodynamics of stacking interactions in proteins

P. Procacci, 2011 .

Vibrational frequencies of C70

P. Procacci, G. Cardini, V. Schettino, 1992 .

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

P. Procacci, Simone Marsili, M. Bizzarri, 2014, Journal of chemical theory and computation.

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

S. Menichetti, P. Procacci, M. Martina, 2013, Journal of medicinal chemistry.

Vibronic interactions in the lowest excited singlet state of C60

G. Marconi, P. Procacci, P. Salvi, 1993 .

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

P. Procacci, 2017, J. Chem. Inf. Model..

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

P. Procacci, Simone Marsili, M. Bizzarri, 2011, The journal of physical chemistry. B.

New Perspective on How and Why Immunophilin FK506-Related Ligands Work

S. Menichetti, P. Procacci, M. Martina, 2011 .

SAMPL9 blind predictions using nonequilibrium alchemical approaches.

G. Guarnieri, P. Procacci, 2022, The Journal of chemical physics.

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

P. Procacci, R. Chelli, 2017, Journal of chemical theory and computation.

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

P. Procacci, 2022, Journal of chemical theory and computation.

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

P. Procacci, M. Pagliai, R. Chelli, 2018, The Journal of chemical physics.

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

A. Rosato, P. Procacci, M. Pagliai, 2020, ACS omega.

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

S. Menichetti, P. Procacci, C. Viglianisi, 2013, The Journal of organic chemistry.

Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?

P. Procacci, 2022, Molecules.

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

R. Livi, P. Procacci, Simone Marsili, 2011, Biopolymers.

A Vibrational Potential Function for Molecular Dynamics Simulation of Buckminsterfullerene

G. Marconi, P. Procacci, G. Cardini, 1993 .

The conformational landscape of tartrate-based inhibitors of the TACE enzyme as revealed by Hamiltonian Replica Exchange simulation.

P. Procacci, C. Guardiani, 2013, Physical chemistry chemical physics : PCCP.

2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study

P. Procacci, E. Fratini, M. Pagliai, 2022, The journal of physical chemistry. A.

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

G. Guarnieri, P. Procacci, M. Pagliai, 2020, Chemical communications.

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

P. Procacci, M. Mannini, G. Pescitelli, 2014, Soft matter.

Empirical force field for the simulation of a class of chromophores in a photosynthetic center

P. Procacci, M. Marchi, M. Ceccarelli, 2001 .

POLAR PHONONS IN SO2 SINGLE CRYSTAL

E. Castellucci, P. Procacci, P. Salvi, 1991 .

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

Simone Marsili, Riccardo Chelli, Piero Procacci, 2007, The Journal of chemical physics.

Computer-aided series expansion for Phonon self-energy

R. Valle, P. Procacci, 2000 .

Molecular dynamics and anharmonic effects in the phonon spectra of solid carbon dioxide

P. Procacci, G. Cardini, R. Righini, 1987 .

Anharmonic calculation of bandwidths and frequency shifts in crystalline CO2

P. Procacci, R. Righini, S. Califano, 1987 .

Vibrational relaxation in crystal SO2

P. Procacci, R. Righini, P. Salvi, 1991 .

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

P. Procacci, M. Pagliai, R. Chelli, 2019, The journal of physical chemistry. B.

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

S. Menichetti, P. Procacci, C. Viglianisi, 2015, Chemical communications.

Glycerol condensed phases Part II.A molecular dynamics study of the conformational structure and hydrogen bonding

Gianni Cardini, Riccardo Chelli, Piero Procacci, 1999 .

Simulated structure, dynamics, and vibrational spectra of liquid benzene

Gianni Cardini, Riccardo Chelli, Piero Procacci, 2000 .

Monte Carlo and Molecular Dynamics Simulations

E. Clementi, P. Procacci, G. Lie, 1989 .

Density Functional Calculation of Structural and Vibrational Properties of Glycerol

Francesco Luigi Gervasio, Riccardo Chelli, Piero Procacci, 2000 .

CRESCO ENEA HPC clusters: a working example of a multifabric GPFS Spectrum Scale layout

Filippo Palombi, Giovanni Ponti, F. Iannone, 2019, 2019 International Conference on High Performance Computing & Simulation (HPCS).

Insights into the Conformational Switching Mechanism of the Human Vascular Endothelial Growth Factor Receptor Type 2 Kinase Domain

Simone Marsili, Piero Procacci, Paola Gratteri, 2012, J. Chem. Inf. Model..

Inhibition of the Main Protease 3CL-pro of the Coronavirus Disease 19 via Structure-Based Ligand Design and Molecular Modeling

P. Procacci, M. Pagliai, Marina Macchiagodena, 2020, 2002.09937.

The nature of intermolecular interactions between aromatic amino acid residues

Francesco Luigi Gervasio, Riccardo Chelli, Piero Procacci, 2002, Proteins.

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

Piero Procacci, P. Procacci, 2016, Physical chemistry chemical physics : PCCP.

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

Simone Marsili, Giorgio Federico Signorini, Riccardo Chelli, 2009, J. Comput. Chem..

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

Riccardo Chelli, Piero Procacci, P. Procacci, 2009, Physical chemistry chemical physics : PCCP.

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

Simone Marsili, Riccardo Chelli, Piero Procacci, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

Simone Marsili, Riccardo Chelli, Piero Procacci, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

Simone Marsili, Riccardo Chelli, Piero Procacci, 2006, The Journal of chemical physics.

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

Piero Procacci, Antonio Rosato, Marco Pagliai, 2019, J. Chem. Inf. Model..

Mycotoxins aptasensing: From molecular docking to electrochemical detection of deoxynivalenol.

G. Marrazza, P. Procacci, M. Pagliai, 2020, Bioelectrochemistry.

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

Francesco Luigi Gervasio, Riccardo Chelli, Piero Procacci, 2002 .

Molecular dynamics of glass-forming liquids: Structure and dynamics of liquid metatoluidine

Gianni Cardini, Riccardo Chelli, Piero Procacci, 2002 .

Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

Piero Procacci, Lorenzo Casbarra, P. Procacci, 2021, Journal of Computer-Aided Molecular Design.

SAMPL7 blind predictions using nonequilibrium alchemical approaches

Piero Procacci, Guido Guarnieri, G. Guarnieri, 2021, Journal of Computer-Aided Molecular Design.

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.

P. Procacci, M. Pagliai, Dario Vassetti, 2019, Journal of chemical theory and computation.

Computer simulation of solid C60 using multiple time‐step algorithms

Piero Procacci, Bruce J. Berne, B. Berne, 1994 .

NE‐RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes

P. Procacci, M. Pagliai, M. Macchiagodena, 2023, J. Comput. Chem..

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

P. Procacci, 2022, Journal of chemical theory and computation.

Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS

P. Procacci, M. Pagliai, Marina Macchiagodena, 2021, J. Chem. Inf. Model..

Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics.

Piero Procacci, P. Procacci, 2020, Current opinion in structural biology.

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

Piero Procacci, P. Procacci, 2019, The Journal of chemical physics.

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

Piero Procacci, P. Procacci, 2016, J. Chem. Inf. Model..

Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to.

Piero Procacci, P. Procacci, 2017, Journal of molecular graphics & modelling.

Reformulating the entropic contribution in molecular docking scoring functions

Piero Procacci, P. Procacci, 2016, J. Comput. Chem..

Electrical response in chemical potential equalization schemes

Riccardo Chelli, Piero Procacci, Roberto Righini, 1999 .

ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions

Piero Procacci, Emanuele Paci, Massimo Marchi, 1997 .

A Very Fast Molecular Dynamics Method To Simulate Biomolecular Systems with Realistic Electrostatic Interactions

Piero Procacci, Massimo Marchi, T. Darden, 1996 .

An ab initio force field for the cofactors of bacterial photosynthesis

Massimo Marchi, Piero Procacci, Matteo Ceccarelli, 2003, J. Comput. Chem..

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations.

Piero Procacci, Chiara Cardelli, P. Procacci, 2014, Journal of chemical theory and computation.

Forecasting market states

Tomaso Aste, Pier Francesco Procacci, T. Aste, 2018, Machine Learning and AI in Finance.

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

Simone Marsili, Riccardo Chelli, Piero Procacci, 2006, The journal of physical chemistry. B.

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

Nohad Gresh, Riccardo Chelli, Piero Procacci, 2007, The journal of physical chemistry. A.

A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge

Piero Procacci, P. Procacci, 2020, Journal of Computer-Aided Molecular Design.

Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion.

A. Barducci, P. Procacci, R. Chelli, 2007, The Journal of chemical physics.

Dynamical and structural correlation in supercooled liquids: A molecular dynamics investigation of m-toluidine

Gianni Cardini, Riccardo Chelli, Piero Procacci, 2003 .

Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease

P. Procacci, M. Pagliai, Marina Macchiagodena, 2021, Journal of Molecular Graphics and Modelling.

Conformational landscape of N-glycosylated peptides detecting autoantibodies in multiple sclerosis, revealed by Hamiltonian replica exchange.

Giorgio F. Signorini, R. Livi, P. Procacci, 2012, The journal of physical chemistry. B.

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

Francesco L Gervasio, Riccardo Chelli, Piero Procacci, 2006, Journal of the American Chemical Society.

Towards a polarizable force field for molecular liquids

Riccardo Chelli, Piero Procacci, Roberto Righini, 2002 .

Inter‐residue and solvent‐residue interactions in proteins: A statistical study on experimental structures

Francesco Luigi Gervasio, Riccardo Chelli, Piero Procacci, 2004, Proteins.

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

R. Livi, P. Procacci, Simone Marsili, 2009, Journal of the American Chemical Society.

Statistical thermodynamic basis in drug-receptor interactions: double annihilation and double decoupling alchemical theories, revisited

P. Procacci, 2016, 1607.03783.

Market structure dynamics during COVID-19 outbreak

Carolyn E. Phelan, T. Aste, P. Procacci, 2020, 2003.10922.

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

Piero Procacci, Guido Guarnieri, Massimiliano Guarrasi, 2018, Journal of Computer-Aided Molecular Design.

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

P. Procacci, 2018, Journal of chemical theory and computation.

Comment on “Classical polarizable force fields parametrized from ab initio calculations” [J. Chem. Phys. 117, 1416 (2002)]

Riccardo Chelli, Piero Procacci, P. Procacci, 2003 .

Interaction between aromatic residues. Molecular dynamics and ab initio exploration of the potential energy surface of the tryptophan-histidine pair

Schettino, F. Gervasio, P. Procacci, 2000 .

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

G. Guarnieri, P. Procacci, M. Pagliai, 2020, Journal of chemical theory and computation.

Vibrational properties of Xe—fullerene adducts. A molecular dynamics approach

P. Procacci, G. Cardini, V. Schettino, 1992 .

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

Piero Procacci, P. Procacci, 2019, Physical chemistry chemical physics : PCCP.

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

P. Procacci, M. Pagliai, R. Chelli, 2017, Journal of chemical theory and computation.

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

P. Procacci, 2016, Physical chemistry chemical physics : PCCP.

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

P. Procacci, R. Chelli, 2009, Physical chemistry chemical physics : PCCP.

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

Piero Procacci, Guido Guarnieri, G. Guarnieri, 2019, Journal of Computer-Aided Molecular Design.

Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions

P. Procacci, 2023, Journal of chemical theory and computation.

Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.

F. Gervasio, P. Procacci, Valerio Rizzi, 2024, The journal of physical chemistry. B.

Comment to “Calculation of the Dipole Moment for Polypeptides Using the Generalized Born-Electronegativity Equalization Method: Results in Vacuum and Continuum-Dielectric Solvent”

Riccardo Chelli, Piero Procacci, P. Procacci, 2004 .

The far-infrared spectrum of crystalline C[sub 60]

P. Procacci, R. Bini, V. Schettino, 1993 .

SAMPL9 blind predictions using nonequilibrium alchemical approaches.

G. Guarnieri, P. Procacci, 2022, The Journal of chemical physics.