Piero Procacci

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 35

Top Topics

Aqueous Solution

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

Journal of computer-aided molecular design

The journal of physical chemistry. B

The Journal of chemical physics

This page only lists publications with an associated author ORCID identifier.

Publications

Zhaoxi Sun, Piero Procacci
Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems. Physical chemistry chemical physics : PCCP 26 (29) (2024)
Giorgio Di Paco, Marina Macchiagodena, Piero Procacci
Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. ChemMedChem (2024)
Giorgio Di Paco, Marina Macchiagodena, Piero Procacci
Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. ChemMedChem 19 (10) (2024)
Maurice Karrenbrock, Valerio Rizzi, Piero Procacci, Francesco Luigi Gervasio
Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. The journal of physical chemistry. B (2024)
Maurice Karrenbrock, Valerio Rizzi, Piero Procacci, Francesco Luigi Gervasio
Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. The journal of physical chemistry. B 128 (7) (2024)
Giorgio Di Paco, Marina Macchiagodena, Piero Procacci
Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. ChemMedChem 19 (10) (2024)
Maurice Karrenbrock, Valerio Rizzi, Piero Procacci, Francesco Luigi Gervasio
Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. The journal of physical chemistry. B 128 (7) (2024)
Zhaoxi Sun, Piero Procacci
Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems. Physical chemistry chemical physics : PCCP (2024)
Piero Procacci, Guido Guarnieri
SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches. The Journal of chemical physics 158 (12) (2023)
Marina Macchiagodena, Marco Pagliai, Piero Procacci
NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes. Journal of computational chemistry 44 (12) (2023)
Marina Macchiagodena, Marco Pagliai, Piero Procacci
NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes. Journal of computational chemistry (2023)
Piero Procacci
Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions. Journal of chemical theory and computation (2023)
Piero Procacci
Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach. Journal of chemical theory and computation 18 (6) (2022)
Marina Macchiagodena, Gavino Bassu, Irene Vettori, Emiliano Fratini, Piero Procacci, Marco Pagliai
2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study. The journal of physical chemistry. A 126 (47) (2022)
Lorenzo Casbarra, Piero Procacci
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges. Journal of computer-aided molecular design 35 (6) (2021)
Piero Procacci, Guido Guarnieri
SAMPL7 blind predictions using nonequilibrium alchemical approaches. Journal of computer-aided molecular design 35 (1) (2021)
Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Piero Procacci
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS. Journal of chemical information and modeling 61 (11) (2021)
Piero Procacci, Marina Macchiagodena
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge. Journal of computer-aided molecular design 35 (10) (2021)
Piero Procacci, Marina Macchiagodena, Marco Pagliai, Guido Guarnieri, Francesco Iannone
Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations. Chemical communications (Cambridge, England) 56 (62) (2020)
Marina Macchiagodena, Marco Pagliai, Maurice Karrenbrock, Guido Guarnieri, Francesco Iannone, Piero Procacci
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. Journal of chemical theory and computation 16 (11) (2020)
Marina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci
Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. Journal of chemical information and modeling 59 (9) (2019)
Marco Pagliai, Giada Funghi, Dario Vassetti, Piero Procacci, Riccardo Chelli, Gianni Cardini
Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration. The journal of physical chemistry. B 123 (18) (2019)
Piero Procacci, Guido Guarnieri
SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches. Journal of computer-aided molecular design 34 (4) (2019)
Marco Pagliai, Marina Macchiagodena, Piero Procacci, Gianni Cardini
Evidence of a Low-High Density Turning Point in Liquid Water at Ordinary Temperature under Pressure: A Molecular Dynamics Study. The journal of physical chemistry letters 10 (20) (2019)
Dario Vassetti, Marco Pagliai, Piero Procacci
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. Journal of chemical theory and computation 15 (3) (2019)
Piero Procacci
Solvation free energies via alchemical simulations: let's get honest about sampling, once more. Physical chemistry chemical physics : PCCP 21 (25) (2019)
Piero Procacci
Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates. The Journal of chemical physics 151 (14) (2019)
Piero Procacci
Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches. The Journal of chemical physics 151 (14) (2019)
Piero Procacci, Massimiliano Guarrasi, Guido Guarnieri
SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach. Journal of computer-aided molecular design 32 (10) (2018)
Edoardo Giovannelli, Cristina Gellini, Giangaetano Pietraperzia, Gianni Cardini, Piero Procacci, Marco Pagliai, Victor V Volkov, Riccardo Chelli
Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states. The Journal of chemical physics 149 (8) (2018)
Piero Procacci
Myeloid Cell Leukemia 1 Inhibition: An in Silico Study Using Non-equilibrium Fast Double Annihilation Technology. Journal of chemical theory and computation 14 (7) (2018)
Edoardo Giovannelli, Matteo Cioni, Piero Procacci, Gianni Cardini, Marco Pagliai, Victor Volkov, Riccardo Chelli
Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation. Journal of chemical theory and computation 13 (12) (2017)
Piero Procacci
PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules. Journal of chemical information and modeling 57 (6) (2017)
Edoardo Giovannelli, Piero Procacci, Gianni Cardini, Marco Pagliai, Victor Volkov, Riccardo Chelli
Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework. Journal of chemical theory and computation 13 (12) (2017)
Piero Procacci, Riccardo Chelli
Statistical Mechanics of Ligand-Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories. Journal of chemical theory and computation 13 (5) (2017)