All Stories

  1. SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches

    Article • The Journal of Chemical Physics, March 2023, American Institute of Physics

    Dr piero procacci

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

    Article • Journal of Chemical Theory and Computation, June 2022, American Chemical Society (ACS)

    Dr piero procacci

  3. SAMPL9 blind predictions using nonequilibrium alchemical approaches

    Article • The Journal of Chemical Physics, April 2022, American Institute of Physics

    Dr piero procacci

  4. Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach

    Article • February 2022, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Journal of Molecular Graphics and Modelling, January 2022, Elsevier

    Dr piero procacci

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

    Article • Journal of Chemical Information and Modeling, November 2021, American Chemical Society (ACS)

    Dr piero procacci

  7. On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge

    Article • Journal of Computer-Aided Molecular Design, October 2021, Springer Science + Business Media

    Dr piero procacci

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

    Article • Journal of Computer-Aided Molecular Design, May 2021, Springer Science + Business Media

    Dr piero procacci

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

    Article • Bioelectrochemistry, April 2021, Elsevier

    Dr piero procacci

  10. SAMPL7 blind predictions using nonequilibrium alchemical approaches

    Article • Journal of Computer-Aided Molecular Design, January 2021, Springer Science + Business Media

    Dr piero procacci

  11. 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

    Article • Journal of Chemical Theory and Computation, October 2020, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • ACS Omega, June 2020, American Chemical Society (ACS)

    Dr piero procacci

  13. Interaction of Hydroxychloroquine with SARS-CoV2 Functional Proteins Using All-atoms Non-equilibrium Alchemical Simulations

    Article • April 2020, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Chemical Communications, January 2020, Royal Society of Chemistry

    Dr piero procacci

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

    Article • Journal of Computer-Aided Molecular Design, October 2019, Springer Science + Business Media

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, October 2019, American Institute of Physics

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, October 2019, American Institute of Physics

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry Letters, October 2019, American Chemical Society (ACS)

    Dr piero procacci, Gianni Cardini

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

    Article • Journal of Chemical Information and Modeling, August 2019, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry B, April 2019, American Chemical Society (ACS)

    Dr piero procacci, Gianni Cardini

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

    Article • The Journal of Chemical Physics, March 2019, American Institute of Physics

    Dr piero procacci

  22. 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

    Article • Journal of Chemical Theory and Computation, January 2019, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Journal of Enzyme Inhibition and Medicinal Chemistry, January 2019, Taylor & Francis

    Dr. Gabriella Caminati, Dr Stefano Menichetti, Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 2019, Royal Society of Chemistry

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, August 2018, American Institute of Physics

    Gianni Cardini, Dr piero procacci

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

    Article • Journal of Computer-Aided Molecular Design, August 2018, Springer Science + Business Media

    Dr piero procacci

  27. Lipid tempering simulation of model biological membranes on parallel platforms

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, July 2018, Elsevier

    Dr piero procacci

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

    Article • Journal of Chemical Theory and Computation, June 2018, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Journal of Chemical Theory and Computation, November 2017, American Chemical Society (ACS)

    Gianni Cardini, Dr piero procacci

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

    Article • Journal of Chemical Theory and Computation, November 2017, American Chemical Society (ACS)

    Gianni Cardini, Dr piero procacci

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

    Article • Journal of Chemical Information and Modeling, June 2017, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Journal of Chemical Theory and Computation, April 2017, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry B, July 2016, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Journal of Chemical Information and Modeling, June 2016, American Chemical Society (ACS)

    Dr piero procacci

  35. Reformulating the entropic contribution in molecular docking scoring functions

    Article • Journal of Computational Chemistry, May 2016, Wiley

    Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 2016, Royal Society of Chemistry

    Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 2016, Royal Society of Chemistry

    Dr piero procacci

  38. Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition

    Article • Journal of Molecular Structure, July 2015, Elsevier

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, April 2015, American Institute of Physics

    Dr piero procacci

  40. Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations

    Article • Journal of Chemical Theory and Computation, January 2015, American Chemical Society (ACS)

    Dr piero procacci

  41. heterohelicene radical cations as redox-driven molecular switches

    Article • Chemical Communications, January 2015, Royal Society of Chemistry

    Dr Stefano Menichetti, Dr Caterina Viglianisi, Dr piero procacci

  42. Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

    Article • Journal of Chemical Theory and Computation, April 2014, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Soft Matter, January 2014, Royal Society of Chemistry

    Dr piero procacci

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

    Article • Journal of Chemical Theory and Computation, November 2013, American Chemical Society (ACS)

    Dr piero procacci

  45. Multiple Bennett acceptance ratio made easy for replica exchange simulations

    Article • The Journal of Chemical Physics, September 2013, American Institute of Physics

    Dr piero procacci

  46. Naphtho[1,2- b :8,7- b ′]- and -[1,2- b :5,6- b ′]dithiophenes

    Article • The Journal of Organic Chemistry, April 2013, American Chemical Society (ACS)

    Dr Caterina Viglianisi, Dr piero procacci

  47. The Precise Chemical–Physical Nature of the Pharmacore in FK506 Binding Protein Inhibition: ElteX, a New Class of Nanomolar FKBP12 Ligands

    Article • Journal of Medicinal Chemistry, January 2013, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Riccardo Chelli, Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry B, April 2012, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Journal of Chemical Information and Modeling, January 2012, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry Letters, October 2011, American Chemical Society (ACS)

    Dr piero procacci

  53. Intraligand Hydrophobic Interactions Rationalize Drug Affinities for Peptidyl−Prolyl Cis−Trans Isomerase Protein

    Article • The Journal of Physical Chemistry B, April 2011, American Chemical Society (ACS)

    Dr piero procacci

  54. Thermodynamics of stacking interactions in proteins

    Article • Annual Reports Section C (Physical Chemistry), January 2011, Royal Society of Chemistry

    Dr piero procacci

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

    Article • Biopolymers, January 2011, Wiley

    Dr piero procacci

  56. Energy dissipation asymmetry in the non equilibrium folding/unfolding of the single molecule alanine decapeptide

    Article • Chemical Physics, September 2010, Elsevier

    Dr piero procacci

  57. Hummer and Szabo-like Potential of Mean Force Estimator for Bidirectional Nonequilibrium Pulling Experiments/Simulations

    Article • The Journal of Physical Chemistry B, July 2010, American Chemical Society (ACS)

    Dr Paolo Nicolini, Dr piero procacci

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

    Article • The Journal of Physical Chemistry B, February 2010, American Chemical Society (ACS)

    Dr piero procacci

  59. Fragment 101−108 of Myelin Oligodendrocyte Glycoprotein: A Possible Lead Compound for Multiple Sclerosis

    Article • Journal of the American Chemical Society, November 2009, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 2009, Royal Society of Chemistry

    Dr piero procacci

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

    Article • Journal of Computational Chemistry, January 2009, Wiley

    Dr piero procacci

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

    Article • Physical Review E, March 2008, American Physical Society (APS)

    Dr piero procacci

  63. Thermodynamics of stacking interactions in proteins

    Article • Physical Chemistry Chemical Physics, January 2008, Royal Society of Chemistry

    Dr piero procacci

  64. Key Role of the Polarization Anisotropy of Water in Modeling Classical Polarizable Force Fields

    Article • The Journal of Physical Chemistry A, August 2007, American Chemical Society (ACS)

    Professor Jean-Philip Piquemal, Dr piero procacci

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

    Article • The Journal of Chemical Physics, July 2007, American Institute of Physics

    Dr piero procacci

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

    Article • Physical Review E, May 2007, American Physical Society (APS)

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, January 2007, American Institute of Physics

    Dr piero procacci

  68. Problems in molecular dynamics of condensed phases

    Article • Theoretical Chemistry Accounts, January 2007, Springer Science + Business Media

    Gianni Cardini, Dr piero procacci

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

    Article • The Journal of Chemical Physics, October 2006, American Institute of Physics

    Dr piero procacci

  70. Self-healing Umbrella Sampling:  A Non-equilibrium Approach for Quantitative Free Energy Calculations

    Article • The Journal of Physical Chemistry B, July 2006, American Chemical Society (ACS)

    Dr piero procacci

  71. Comment on “From Subtle to Substantial:  Role of Metal Ions on π−π Interactions”

    Article • The Journal of Physical Chemistry B, May 2006, American Chemical Society (ACS)

    Dr piero procacci

  72. Metadynamics Simulation of Prion Protein:  β-Structure Stability and the Early Stages of Misfolding

    Article • Journal of the American Chemical Society, March 2006, American Chemical Society (ACS)

    Dr piero procacci

  73. Matteo Ceccarelli, Piero Procacci, Massimo Marchi "Anab initio force field for the cofactors of bacterial photosynthesis,"Journal of Computational Chemistry(2003)24(2) 129-142.

    Article • Journal of Computational Chemistry, January 2006, Wiley

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, November 2005, American Institute of Physics

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, June 2005, American Institute of Physics

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, February 2005, American Institute of Physics

    Gianni Cardini, Dr piero procacci

  77. Misfolding Pathways of the Prion Protein Probed by Molecular Dynamics Simulations

    Article • Biophysical Journal, February 2005, Elsevier

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry B, October 2004, American Chemical Society (ACS)

    Dr piero procacci

  79. Energetic Fitness of Histidine Protonation States in PDB Structures

    Article • The Journal of Physical Chemistry B, August 2004, American Chemical Society (ACS)

    Dr piero procacci

  80. Inter-residue and solvent-residue interactions in proteins: A statistical study on experimental structures

    Article • Proteins Structure Function and Bioinformatics, February 2004, Wiley

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, July 2003, American Institute of Physics

    Gianni Cardini, Dr piero procacci

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

    Article • The Journal of Chemical Physics, January 2003, American Institute of Physics

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, November 2002, American Institute of Physics

    Dr piero procacci

  84. The nature of intermolecular interactions between aromatic amino acid residues

    Article • Proteins Structure Function and Bioinformatics, May 2002, Wiley

    Dr piero procacci

  85. Stacking and T-shape Competition in Aromatic−Aromatic Amino Acid Interactions

    Article • Journal of the American Chemical Society, May 2002, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • The Journal of Chemical Physics, April 2002, American Institute of Physics

    Gianni Cardini, Dr piero procacci

  87. Towards a polarizable force field for molecular liquids

    Article • Journal of Molecular Liquids, April 2002, Elsevier

    Dr piero procacci

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

    Article • The Journal of Physical Chemistry A, March 2002, American Chemical Society (ACS)

    Dr piero procacci

  89. Anab initio force field for the cofactors of bacterial photosynthesis

    Article • Journal of Computational Chemistry, January 2002, Wiley

    Dr piero procacci

  90. 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 • The Journal of Physical Chemistry B, August 2001, American Chemical Society (ACS)

    Dr piero procacci

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

    Article • Computational Materials Science, March 2001, Elsevier

    Dr piero procacci

  92. Comment on “Efficient stress relaxation in molecular dynamics simulations of semiflexiblen-alkanes” [Phys. Rev. E.58, 6766 (1998)]

    Article • January 2001, American Physical Society (APS)

    Dr piero procacci

  93. Computer-Aided Series Expansion for Phonon Self-Energy

    Article • Journal of Computational Physics, December 2000, Elsevier

    Dr piero procacci

  94. Simulated structure, dynamics, and vibrational spectra of liquid benzene

    Article • The Journal of Chemical Physics, October 2000, American Institute of Physics

    Gianni Cardini, Dr piero procacci

  95. Density Functional Calculation of Structural and Vibrational Properties of Glycerol

    Article • The Journal of Physical Chemistry A, June 2000, American Chemical Society (ACS)

    Gianni Cardini, Dr piero procacci

  96. Glycerol condensed phases Part I. A molecular dynamics study

    Article • Physical Chemistry Chemical Physics, January 1999, Royal Society of Chemistry

    Gianni Cardini, Dr piero procacci

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

    Article • Physical Chemistry Chemical Physics, January 1999, Royal Society of Chemistry

    Gianni Cardini, Dr piero procacci

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

    Article • The Journal of Chemical Physics, October 1998, American Institute of Physics

    Dr piero procacci

  99. Modeling the solvent effect in electronic transitions

    Article • June 1998, World Scientific Pub Co Pte Lt

    Dr piero procacci

  100. Efficient calculation of high-order self-energy corrections to phonon linewidths: Application to α-nitrogen

    Article • May 1993, American Physical Society (APS)

    Dr piero procacci

  101. Vibronic interactions in the lowest excited singlet state of C60

    Article • Journal of Molecular Structure, March 1993, Elsevier

    Dr piero procacci

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

    Article • Chemical Physics Letters, November 1992, Elsevier

    Gianni Cardini, Dr piero procacci

  103. Equation of motion for the Green’s function in anharmonic solids

    Article • September 1992, American Physical Society (APS)

    Dr piero procacci

  104. Vibrational frequencies of C70

    Article • Chemical Physics Letters, July 1992, Elsevier

    Gianni Cardini, Dr piero procacci

  105. A general algorithm for computing Voronoi volumes: Application to the hydrated crystal of myoglobin

    Article • International Journal of Quantum Chemistry, June 1992, Wiley

    Dr piero procacci

  106. Anharmonic lattice dynamics and computer simulation for simple model systems

    Article • February 1992, American Physical Society (APS)

    Gianni Cardini, Dr piero procacci

  107. Vibrational relaxation in crystal SO2

    Article • Chemical Physics, July 1991, Elsevier

    Dr piero procacci

  108. Polar phonons in SO2 single crystal

    Article • Chemical Physics, March 1991, Elsevier

    Dr piero procacci

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

    Article • Chemical Physics, November 1987, Elsevier

    Gianni Cardini, Dr piero procacci

  110. Anharmonic calculation of bandwidths and frequency shifts in crystalline CO2

    Article • Chemical Physics, September 1987, Elsevier

    Dr piero procacci