Personale

Recapiti

Orario di ricevimento

Italiano

Curriculum

Pubblicazioni

Insegnamenti

English

Curriculum

Piero PROCACCI

Ruolo attuale:: Professore Associato
SSD:: CHEM-02/A - Chimica fisica
Afferenza organizzativa:: Dipartimento di Chimica 'Ugo Schiff' - DICUS

Recapiti

	0554573081
	piero.procacci(AT)unifi.it

Piero PROCACCI

Curriculum

DATI PERSONALI

- Cognome: Procacci
- Nome: Piero
- Nascita: 23 gennaio 1961 a Roma
- Cittadinanza: Italiana
- Indirizzo: Chemistry Dept., University of Florence, Via Lastruccia n. 3, Sesto F.no
- Tel: 055-4573081
- Email: procacci@unifi.it

EDUCAZIONE

- 1979: Diploma di Maturita', Liceo Classico
- 1986: Laurea in Chimica, Universita' di Firenze
- 1993: Dottorato in Chimica, Universita' di Firenze

IMPIEGHI PROFESSIONALI ED ACCADEMICI

- Gennaio 1988 - Agosto 1989: Ricercatore presso Department of Scientific and Engineering Computations, IBM corporation, Kingston NY (USA), diretto dal Prof. Enrico Clementi
- Luglio 1993 - Giugno 1994: PostDoctoral Fellow presso il Dipartimento di Chimica della Columbia University (gruppo del Prof. Bruce J. Berne), New York NY (USA)
- Ottobre 1994 - Dicembre 1996: PostDoctoral Fellow presso il Centro Europeo di Calcolo Atomico e Molecolare (CECAM), Ecole Normale Superieure, Lyon (FRANCE)
- Gennaio 1997 - Settembre 2001: Ricercatore presso il Dipartimento di Chimica dell'Universita' di Firenze
- Settembre 2001 - : Professore Associato presso il Dipartimento di Chimica dell'Universita' di Firenze

FINANZIAMENTI (come PI) E PREMI

- Febbraio 1993: Consiglio Delle Ricerche, Vincitore di una borsa (bando nazionale) in Chimica-Fisica (38/50 points)
- Marzo 1996: Vincitore di una Borsa TMR erogata dalla Comunita' Europea (Training and Mobility Grant n. FMBI950363) per il progetto: Electronic transitions in the photosynthetic reaction center
- Settembre 2001: Idoneita' per Professore di seconda fascia (Bando Nazionale)
- Aprile 2004: Conferma nel ruolo di Professore Associato in Chimica-Fisica, Universita' di Firenze
- Ottobre 2009: Finanziamento per Euro 156000 dalla Regione Toscana nell'ambito del Bando Salute 2009 sul progetto dal totolo "In silico Assessment of peptides with potential pharmaceutical properties for Multiple Sclerosis."
- Giugno 2011: Allocazione di tempo di calcolo a seguito del bando competitivo CINECA-ISCRA-B (Grant HP10BDV7I7-FKBP12-L) per il progetto: "Determining the binding affinities for drug receptor complexes at the full atomistic level using solute tempering and multiple Bennett acceptance ratio : the case of FKBP12 tacrolimous related ligands"
- Gennaio 2014: Consguimento della Abilitazione Scientifica Nazionale per Professore di Prima Fascia nel settore scientifico 03/A2, Chimica Fisica
- Giugno 2015: Allocazione di tempo di calcolo a seguito del bando competitivo CINECA-ISCRA-C Grant HP10CSNWHM- MPNEDRUG oper il Progetto "An Hybrid MPI and OpenMP parallel non-equilibrium method for fast calculations of the binding free energy in Molecular Dynamics Simulations of ligand-receptor systems"
- Luglio 2016: Allocazione di tempo di calcolo a seguito del bando competitivo CINECA-ISCRA-B Grant INHITACE - HP10BH62LR per il Progetto "Design of new small inhibitors for the tumor necrosis factor-alpha converting enzyme: a possible route for controlling the inflammatory response in autoimmune diseases."
- Gennaio 2017: Consguimento della Abilitazione Scientifica Nazionale per Professore di Prima Fascia nel settore scientifico 02/B2 (Fisica teorica della materia)
- Ottobre 2017 Vincitore della 15esima Call PRACE (Partnership for Advance Computing in Europe) con allocazione di 17,000,000 of core hours su piattaforme Tier-0 per il Progetto "Drug design for HPC systems: Fast Switching Double Annihilation Method (FS-DAM) at work" www.prace-ri.eu
- Dicembre 2017 Allocazione di tempo di calcolo a seguito del bando competitivo CINECA-ISCRA-C Grant F-SAMPL6-HP10CG5AD "Fast swicthing double annihilation in the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL6) challenge"

INCARICHI DI PEER-REVIEW

- Journal of the American Chemical Society
- Physical Chemistry Chemical Physics
- Journal of Chemical Teory and Computation
- Journal of Chemical Information and Modeling
- Journal of Chemical Physics
- Journal of Physical Chemistry
- Chemical Physics
- Physical Review Letters
- Referee per ERC Consolidator Grant 2013, ERC Sectors PE4_13, PE4_15, LS7_3)
- Referee per The Partnership for Advanced Computing in Europe (PRACE), ERC Sectors PE4_13, PE4_15, LS7_3
- Referee per Italian Super-Computing Resource Allocation (ISCRA)
- Referee per Italian Bando FIRB, (PE4_13, PE4_15 ERC-based sectors)

COLLABORAZIONI SCIENTIFICHE

- European Laboratory of non Linear Spectroscopy (LENS), Firenze
- Dipartumento di Fisica, Universita' di Firenze
- Dipartimento di Neuroscienze, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence
- Sviluppo Sistemi per l'informatica e l'ITC della Agenzia nazionale Nuove Tecnologie (ENEA)
- Laboratoire bioénergétique membranaire et stress (LBMS), Centre D'Etudes, CEA Sacly Gif Sur Yvette (France)
- Department of Chemistry and Applied Biosciences, ETH Zurich (Switzerland), Prof. Michele Parrinello's Group
- Centre Europeen de Calcul Atomic et Moleculaire (CECAM), Ecole Normale Superieure, Lyon (FRANCE)

PRINCIPALI CAMPI DI RICERCA (Settori ERC):

- PE3_17 Statistical physics (condensed matter)
- PE4_13 Physical chemistry of biological systems
- PE4_15 Theoretical and computational chemistry
- LS2_14 Biological systems analysis, modeling and simulation
- LS7_3 Pharmacology, pharmacogenomics, drug discovery and design, drug therapy

ATTIVITA' DI RICERCA E RELATIVI DATI BIBLIOMETRICI

- co-autore o autore di 95 pubblicazioni su Riviste Internazionali con peer-review, indicizzate da ISI/SCOPUS Databases.
- co-autore di 11 contributi in Collezioni o Libri scientifici.
- co-autore del programma ORAC per la simulazione di dinamica molecolare di sistemi di interesse biologico (www.chim.unifi.it/orac)
- Citazioni totali su Google 3207 (h-index 33)
- Citrazioni totali su Scopus 2432 (h-index 30)

Piero PROCACCI

Pubblicazioni

Legenda

Contributo su rivista |

Articolo su libro |

Libro |

Contributo in atti di convegno (proceeding) |

Brevetto |

Curatela | Altro

Altro |

Tesi di Dottorato

Marina Macchiagodena, Marco Pagliai, Piero Procacci (2025). High Performance Computing on CRESCO infrastructure: research activities and results 2023. In: Marina Macchiagodena, Marco Pagliai, Piero Procacci. High Performance Computing on CRESCO infrastructure: research activities and results 2023, pp. 107-113, Roma: ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ISBN:978-88-8286-494-1. Accesso ONLINE all'editore

Di Paco, Giorgio; Macchiagodena, Marina; Procacci, Piero (2024). Identification of Potential inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. CHEMMEDCHEM, vol. .., pp. 1-10, ISSN:1860-7187 DOI

Karrenbrock, Maurice; Rizzi, Valerio; Procacci, Piero; Gervasio, Francesco Luigi (2024). Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. -, pp. 1-11, ISSN:1520-6106 DOI Accesso ONLINE all'editore

Sun, Zhaoxi; Procacci, Piero (2024). Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host–guest systems. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. -, pp. 1-12, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Procacci, Piero; Guarnieri, Guido (2023). SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches. THE JOURNAL OF CHEMICAL PHYSICS, vol. 158, pp. 124117-1-124117-12, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Macchiagodena, Marina; Pagliai, Marco; Procacci, Piero (2023). 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, vol. ..., pp. 1-10, ISSN:1096-987X DOI

Procacci, Piero (2023). Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 19, pp. 8942-8954, ISSN:1549-9618 DOI Accesso ONLINE all'editore

Piero Procacci (2023). High performance computing on CRESCO Infrastructure: research activity and results 2022. In: Piero Procacci, Guido Guarnieri. High Performance Computing on CRESCO infrastructure: research activity and results 2022, pp. 123-126, Frascati (RM) Italia: ENEA - Agenzia nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile, ISBN:9788882864583. Accesso ONLINE all'editore

Procacci, Piero (2022). Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?. MOLECULES, vol. 27, pp. 0-010.3390/molecules27144426, ISSN:1420-3049 DOI Accesso ONLINE all'editore

Procacci, Piero (2022). Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 18, pp. 4014-4026, ISSN:1549-9626 DOI

Macchiagodena, Marina; Bassu, Gavino; Vettori, Irene; Fratini, Emiliano; Procacci, Piero; Pagliai, Marco (2022). 2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 126, pp. 8826-8833, ISSN:1089-5639 DOI Accesso ONLINE all'editore

Macchiagodena, Marina; Pagliai, Marco; Procacci, Piero (2022). Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, vol. 110, pp. 108042-108050, ISSN:1093-3263 DOI

Procacci, Piero; Guarnieri, Guido (2022). SAMPL9 blind predictions using nonequilibrium alchemical approaches. THE JOURNAL OF CHEMICAL PHYSICS, vol. 156, pp. 164104-164104, ISSN:0021-9606 DOI

Macchiagodena M.; Karrenbrock M.; Pagliai M.; Procacci P. (2021). Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS. JOURNAL OF CHEMICAL INFORMATION AND MODELING, vol. 61, pp. 5320-5326-53260.1021/acs.jcim.1c00909, ISSN:1549-9596 DOI

Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Guido Guarnieri, Francesco Iannone, Piero Procacci (2021). Nonequilibrium Alchemical Simulations for the Development of Drugs Against Covid-19. In: Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Guido Guarnieri, Francesco Iannone, Piero Procacci. Methods in Pharmacology and Toxicology, pp. 1-41, New York, NY.: Springer Nature. Accesso ONLINE all'editore

Piero Procacci (2021). High Performance Computing on CRESCO Infrastructure research activities and results 2019. In: Piero Procacci , Guido Guarnieri. NONEQUILIBRIUM ALCHEMY IN SAMPL7 CHALLENGE, pp. 1-7, Portici: ENEA, DTE-ICT-HPC. Accesso ONLINE all'editore

Subak H.; Selvolini G.; Macchiagodena M.; Ozkan-Ariksoysal D.; Pagliai M.; Procacci P.; Marrazza G. (2021). Mycotoxins aptasensing: From molecular docking to electrochemical detection of deoxynivalenol. BIOELECTROCHEMISTRY, vol. 138, pp. 107691-107691, ISSN:1567-5394 DOI

Procacci P.; Guarnieri G. (2021). SAMPL7 blind predictions using nonequilibrium alchemical approaches. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, pp. 1-11, ISSN:0920-654X DOI Accesso ONLINE all'editore

piero procacci (2021). Blind Predictions for the SAMPL9 Host-Guest Challenge. In: Piero Procacci. High Performance Computing on CRESCO Infrastructure: research activity and results 2020, pp. 116-121, Roma: ENEA, ISBN:978-88-8286-429-3.

Casbarra L.; Procacci P. (2021). 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, pp. 1-8, ISSN:0920-654X DOI Accesso ONLINE all'editore

Procacci, Piero; Macchiagodena, Marina (2021). On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, pp. 1-11, ISSN:0920-654X DOI Accesso ONLINE all'editore

Procacci P. (2021). Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics. CURRENT OPINION IN STRUCTURAL BIOLOGY, vol. 67, pp. 127-134, ISSN:0959-440X DOI

Piero Procacci, Marina Macchiagodena, Marco Pagliai (2021). HPC-DRIVEN HIT-TO-LEAD PROCESS FOR SARS-COV-2 MAIN PROTEASE INHIBITION. In: Piero Procacci, Marina Macchiagodena1,Maurice Karrenbrock2, Marco Pagliai , Guido Guarnieri, Francesco Iannone. ENEA CRESCO in the fight against COVID-19, pp. 32-43, Roma (Italy): ENEA, ISBN:978-88-8286-415-6. Accesso ONLINE all'editore

Caminati, Gabriella; Procacci, Piero; Menichetti, Stefano; Martina, Maria Raffaella; Marsili, Laura (2020). A compound for the determination of the protein FKBP12 and a sensor unit comprising it. Numero: WO 2021124269 Caminati Gabriella, Procacci Piero, Menichetti Stefano, Martina Maria Raffaella, Marsili Laura

Procacci P.; Macchiagodena M.; Pagliai M.; Guarnieri G.; Iannone F. (2020). Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations. CHEMICAL COMMUNICATIONS, vol. 56, pp. 8854-8856, ISSN:1359-7345 DOI

Macchiagodena M.; Pagliai M.; Andreini C.; Rosato A.; Procacci P. (2020). Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. ACS OMEGA, vol. 5, pp. 15301-15310, ISSN:2470-1343 DOI

Procacci P. (2020). A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 34, pp. 635-639, ISSN:0920-654X DOI

Caminati G.; Procacci P. (2020). Mounting evidence of FKBP12 implication in neurodegeneration. NEURAL REGENERATION RESEARCH, vol. 15, pp. 2195-2202, ISSN:1673-5374 DOI

Macchiagodena M.; Pagliai M.; Procacci P. (2020). Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling. CHEMICAL PHYSICS LETTERS, vol. 750, pp. 137489-137489, ISSN:0009-2614 DOI

Procacci, Piero; Guarnieri, Guido (2020). SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. 34, pp. 371-384, ISSN:0920-654X DOI

Macchiagodena, Marina; Pagliai, Marco; Karrenbrock, Maurice; Guarnieri, Guido; Iannone, Francesco; Procacci, Piero (2020). 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, vol. .., pp. 1-13, ISSN:1549-9618 DOI Accesso ONLINE all'editore

Piero Procacci (2020). CRESCO ENEA HPC clusters: a working example of a multifabric GPFS Spectrum Scale layout. In: F.Iannone , F.Ambrosino , G.Bracco, M.De Rosa , A.Funel , G.Guarnieri , S.Migliori , F.Palombi , G.Ponti , G.Santomauro, P. Procacci. 2019 International Conference on High Performance Computing Simulation (HPCS), CRESCO ENEA HPC clusters: a working example of a multifabric GPFS Spectrum Scale layout, pp. 1051-1052, Dublino: IEEE. DOI Accesso ONLINE all'editore

Procacci, Piero (2019). Solvation free energies via alchemical simulations: let's get honest about sampling, once more. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 21, pp. 13826-13834, ISSN:1463-9076 DOI Accesso ONLINE all'editore

MacChiagodena M.; Pagliai M.; Andreini C.; Rosato A.; Procacci P. (2019). 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, vol. 59, pp. 3803-3816, ISSN:1549-9596 DOI Accesso ONLINE all'editore

Pagliai, Marco; Funghi, Giada; Vassetti, Dario; Procacci, Piero; Chelli, Riccardo; Cardini, Gianni (2019). Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 123, pp. 4055-4064, ISSN:1520-6106 DOI Accesso ONLINE all'editore

Pagliai M.; Macchiagodena M.; Procacci P.; Cardini G. (2019). 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, vol. 10, pp. 6414-6418, ISSN:1948-7185 DOI Accesso ONLINE all'editore

Vassetti, Dario; Pagliai, Marco; Procacci, Piero (2019). 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 drug-like organic molecules. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 15, pp. 1983-1995, ISSN:1549-9618 DOI Accesso ONLINE all'editore

Piero Procacci (2019). Comment on ``Statistical efficiency of methods for computing free energy of hydration''[ J. Chem. Phys. 149, 144111 (2018)]. THE JOURNAL OF CHEMICAL PHYSICS, vol. 149, pp. 144111-144113, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Procacci, Piero (2019). Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches. THE JOURNAL OF CHEMICAL PHYSICS, vol. 151, pp. 144113-1-144113-13, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Procacci, Piero (2019). Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates. THE JOURNAL OF CHEMICAL PHYSICS, vol. 151, pp. 144115-1-144115-12, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Gabriella Caminati, Maria Raffaella Martina, Stefano Menichetti, Piero Procacci (2019). Blocking the FKBP12 induced dendrimeric burst in aberrant aggregation of α-synuclein by using the ElteN378 synthetic inhibitor. JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, vol. 34, pp. 1711-1715, ISSN:1475-6366 Accesso ONLINE all'editore

Procacci, Piero; Guarnieri, Guido (2019). SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, vol. ?, pp. 1-12, ISSN:0920-654X DOI Accesso ONLINE all'editore

Cardelli, Chiara; Barducci, Alessandro; Procacci, Piero* (2018). Lipid tempering simulation of model biological membranes on parallel platforms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, vol. 1860, pp. 1480-1488, ISSN:0005-2736 DOI Accesso ONLINE all'editore

Giovannelli, Edoardo; Gellini, Cristina; Pietraperzia, Giangaetano; Cardini, Gianni; Procacci, Piero; Pagliai, Marco; Volkov, Victor; Chelli, Riccardo (2018). 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, vol. 149, pp. 084101-1-084101-7, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Procacci, Piero; Guarrasi, Massimiliano; Guarnieri, Guido (2018). SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, pp. 965-982, ISSN:0920-654X DOI Accesso ONLINE all'editore

Procacci Piero (2018). Myeloid cell leukemia 1 inhibition: An in silico study using nonequilibrium fast double annihilation technology. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 14, pp. 3890-3902-3902, ISSN:1549-9618 DOI

Procacci, Piero (2017). 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, pp. 1-8, ISSN:1549-9596 DOI

Procacci, Piero (2017). Alchemical determination of drug-receptor binding free energy: where we stand and where we could move to. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, vol. 71, pp. 233-241, ISSN:1093-3263 DOI Accesso ONLINE all'editore

Giovannelli, Edoardo; Procacci, Piero; Cardini, Gianni; Pagliai, Marco; Volkov, Victor; Chelli, Riccardo (2017). Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 13, pp. 5874-5886, ISSN:1549-9618 DOI Accesso ONLINE all'editore

Procacci, Piero; Chelli, Riccardo (2017). Statistical Mechanics of Ligand-Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 13, pp. 1924-1933, ISSN:1549-9618 DOI Accesso ONLINE all'editore

Piero Procacci (2017). Characterization of MCL1 inhibition via Fast Switching Double annihilation technology on the CRESCO3 cluster. In: Michele Gusso ed.. High Performance Computing on CRESCO infrastructure: research activities and results 2016, pp. 195-201, Frascati: ENEA, ISBN:978-88-8286-362-3. Accesso ONLINE all'editore

Giovannelli, Edoardo; Cioni, Matteo; Procacci, Piero; Cardini, Gianni; Pagliai, Marco; Volkov, Victor; Chelli, Riccardo (2017). 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, vol. 13, pp. 5887-5899, ISSN:1549-9626 DOI Accesso ONLINE all'editore

Procacci, Piero (2016). Statistical thermodynamic basis in drug-receptor interactions: double annihilation and double decoupling alchemical theories, revisited. pp. 0-0 Accesso ONLINE all'editore

Nerattini, Francesca; Chelli, Riccardo; Procacci, Piero (2016). II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 18, pp. 15005-15018, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Procacci, Piero (2016). Reformulating the entropic contribution in molecular docking scoring functions. JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 37, pp. 1819-27-1827, ISSN:0192-8651 DOI Accesso ONLINE all'editore

Procacci, Piero (2016). Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations. JOURNAL OF CHEMICAL INFORMATION AND MODELING, vol. 56, pp. 1117-1121, ISSN:1549-9596 DOI Accesso ONLINE all'editore

Procacci, Piero (2016). I. Dissociation free energies of drug-receptor systems: Via non-equilibrium alchemical simulations: A theoretical framework. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 18, pp. 14991-15004, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Marsili, Simone; Procacci, Piero (2016). Correction to "Free Energy Reconstruction in Bidirectional Force Spectroscopy Experiments: The Effect of the Device Stiffness". JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, pp. 0-0, ISSN:1520-6106 DOI

Piero Procacci (2016). Fast switching alchemical simulations: a non equilibrium approach for drug discovery projects on parallel platforms. In: Giovanni Ponti, Ed.. High Performance Computing on CRESCO infrastructure: research activities and results 2015, pp. 115-123, Frascati: ENEA, ISBN:978-88-8286-342-5. Accesso ONLINE all'editore

Robert B. Sandberg; Martina Banchelli; Carlo Guardiani; Stefano Menichetti; Gabriella Caminati; Piero Procacci (2015). Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 11, pp. 423-435, ISSN:1549-9618 DOI Accesso ONLINE all'editore

Menichetti, S.; Cecchi, S.; Procacci, P.; Innocenti, M.; Becucci, L.; Franco, L.; Viglianisi, C. (2015). Thia-bridged triarylamine heterohelicene radical cations as redox-driven molecular switches. CHEMICAL COMMUNICATIONS, vol. 51, pp. 11452-11454, ISSN:1359-7345 DOI

Procacci, Piero (2015). Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures. THE JOURNAL OF CHEMICAL PHYSICS, vol. 142, pp. 154117-1-154117-11, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Banchelli, Martina; Guardiani, Carlo; Sandberg, Robert B.; Menichetti, Stefano; Procacci, Piero; Caminati, Gabriella (2015). Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition. JOURNAL OF MOLECULAR STRUCTURE, vol. 1091, pp. 65-73, ISSN:0022-2860 DOI Accesso ONLINE all'editore

Chiara Cardelli; Alessandro Barducci; Piero Procacci (2015). Boosting conformational sampling in lipid bilayer simulations using hamiltonian replica exchange. In: Agostino Funel. High Performance Computing on cresco infrastructure: research activities and results 2013, pp. 183-191 ENEA, ISBN:9788882863128.

Chelli, Riccardo; Cardini, Gianni; Giovannelli, Edoardo; Signorini, Giorgio F.; Procacci, Piero (2015). Implementations of nonequilibrium methods for free energy calculations: forthcoming developments of the ORAC molecular dynamics simulation code. VIRT&L-COMM, vol. 7, pp. 0-0, ISSN:2279-8773 Accesso ONLINE all'editore

Procacci, Piero; Caminati, Gabriella (2015). A coarse grain model for alpha-synuclein aggregation in "High Performance Computing on CRESCO infrastructure: research activities and results 2014". In: Piero Procacci, Gabriella Caminati. High Performance Computing on CRESCO infrastructure: research activities and results 2014, pp. 98-107 ENEA - Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo economico sostenibile, ISBN:9788882863258. Accesso ONLINE all'editore

Piero Procacci;Marco Bizzarri;Simone Marsili (2014). Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 10, pp. 439-450, ISSN:1549-9618 DOI

L. Lascialfari;D. Berti;A. Brandi;S. Cicchi;M. Mannini;G. Pescitelli;P. Procacci (2014). Chiral/ring closed vs. achiral/open chain triazine-based organogelators: induction and amplification of supramolecular chirality in organic gels. SOFT MATTER, vol. 10, pp. 3762-3770, ISSN:1744-683X DOI

Piero Procacci;Chiara Cardelli (2014). Fast Switching Alchemical Transformations in Molecular Dynamics Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 10, pp. 2813-2823, ISSN:1549-9618 DOI

Caterina, Viglianisi; Lucia, Becucci; Faggi, Cristina; Sara, Piantini; Piero, Procacci; Stefano, Menichetti (2013). Regioselective Electrophilic Access to Naphtho[1,2-b:8,7-b′]- and -[1,2-b:5,6-b′]dithiophenes. JOURNAL OF ORGANIC CHEMISTRY, vol. 78, pp. 3496-3502, ISSN:0022-3263 DOI

Carlo Guardiani;Piero Procacci (2013). The conformational landscape of tartrate-based inhibitors of the TACE enzyme as revealed by Hamiltonian Replica Exchange simulation. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 15, pp. 9186-9196, ISSN:1463-9076 DOI

Piero Procacci (2013). Multiple Bennett acceptance ratio made easy for replica exchange simulations. THE JOURNAL OF CHEMICAL PHYSICS, vol. 139, pp. 124105-1-124105-6, ISSN:0021-9606 DOI

Maria Raffaella Martina; Eleonora Tenori; Marco Bizzarri; Stefano Menichetti; Gabriella Caminati; Piero Procacci (2013). The Precise Chemical−Physical Nature of the Pharmacore in FK506 Binding Protein Inhibition: ElteX, a New Class of Nanomolar FKBP12 Ligands. JOURNAL OF MEDICINAL CHEMISTRY, vol. 56, pp. 1041-1051, ISSN:0022-2623 DOI

Martina Banchelli;Carlo Guardiani;Eleonora Tenori;Stefano Menichetti;Gabriella Caminati;Piero Procacci (2013). Chemical–physical analysis of a tartrate model compound for TACE inhibition. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 15, pp. 18881-18893, ISSN:1463-9076 DOI Accesso ONLINE all'editore

M. Chioccioli; S. Marsili; C. Bonaccini; P. Procacci; P. Gratteri (2012). Insights into the Conformational Switching Mechanism of the Human Vascular Endothelial Growth Factor Receptor Type 2 Kinase Domain. JOURNAL OF CHEMICAL INFORMATION AND MODELING, vol. 52, pp. 483-491, ISSN:1549-960X DOI

Carlo Guardiani;Giorgio F. Signorini;Roberto Livi;Anna Maria Papini;Piero Procacci (2012). Conformational Landscape of N-Glycosylated Peptides Detecting Autoantibodies in Multiple Sclerosis, Revealed by Hamiltonian Replica Exchange. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 116, pp. 5458-5467, ISSN:1520-6106 DOI Accesso ONLINE all'editore

C. Guardiani; P. Procacci (2012). Computational Characterization of tartrate-based TACE inhibitors. In: C. Guardiani, P. Procacci. High Performance Computing on CRESCO infrastructure: research activities and results 2010-2011, pp. 37-44, Frascati: Delinda Piccinelli, Enea, UTICT-PRA, Cr Frascati, ISBN:9788882862688. DOI

Carlo Guardiani; Simone Marsili; Stefania Marchetti; Cecilia Gambi; Piero Procacci; Roberto Livi (2011). Conformational structure of the MOG-derived peptide 101–108 in solution. PEPTIDE SCIENCE, vol. 96, pp. 245-251, ISSN:1344-7661 DOI

Marco Bizzarri; Eleonora Tenori; Maria Raffaella Martina; Simone Marsili; Gabriella Caminati; Stefano Menichetti; Piero Procacci (2011). New Perspective on How and Why Immunophilin FK506-Related Ligands Work. THE JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 2, pp. 2834-2839, ISSN:1948-7185 DOI

Marco Bizzarri; Simone Marsili; Piero Procacci (2011). Intraligand Hydrophobic Interactions Rationalize Drug Affinities for Peptidyl−Prolyl Cis−Trans Isomerase Protein. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 115, pp. 6193-6201, ISSN:1520-6106 DOI

Piero Procacci (2011). Thermodynamics of stacking interactions in proteins. ANNUAL REPORTS ON THE PROGRESS OF CHEMISTRY. SECTION C, PHYSICAL CHEMISTRY, vol. 107, pp. 242-262, ISSN:0260-1826 DOI Accesso ONLINE all'editore

Simone Marsiili; Piero Procacci (2011). Improving free energy perturbation methods through multiple state sampling: the histidine tautomerism case. In: Simone Marsili, Piero Procacci. High performance Computing on CRESCO infrastructure: research activities and results 2009-2010, pp. 137-144, Frascati: ENEA, Agenzia Nazionale per le nuove tecnologie, ISBN:9788882862428. Accesso ONLINE all'editore

C. Guardiani; S. Marsili; S. Marchetti; C. M. C. Gambi; P. Procacci; R. Livi (2010). Conformational structure of the MOG-derived peptide 101-108 in solution. PEPTIDE SCIENCE, vol. 96, pp. 245-251, ISSN:1344-7661

Marsili, Simone; Signorini, F. Giorgio; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero (2010). ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level. JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 31, pp. 1106-1116, ISSN:0192-8651 DOI Accesso ONLINE all'editore

Nicolini, Paolo; Procacci, Piero; Chelli, Riccardo (2010). Hummer and Szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 114, pp. 9546-9554, ISSN:1520-6106 DOI Accesso ONLINE all'editore

P. Procacci; S. Marsili (2010). Energy dissipation asymmetry in the non equilibrium folding/unfolding of the single molecule alanine decapeptide. CHEMICAL PHYSICS, vol. 375, pp. 8-15, ISSN:0301-0104 DOI

S. Marsili; P. Procacci (2010). Free Energy Reconstruction in Bidirectional Force Spectroscopy Experiments: The Effect of the Device Stiffness. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 114, pp. 2506-2516, ISSN:1520-6106 DOI

C. Guardiani; S. Marsili; P. Procacci; R. Livi (2009). Fragment 101−108 of Myelin Oligodendrocyte Glycoprotein: A Possible Lead Compound for Multiple Sclerosis. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 131, pp. 17176-17184, ISSN:0002-7863 DOI

Chelli, Riccardo; Procacci, Piero (2009). A potential of mean force estimator based on nonequilibrium work exponential averages. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, pp. 1152-1158, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Marsili, Simone; Procacci, Piero (2008). Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators. PHYSICAL REVIEW E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS, vol. 77, pp. 031104-1-031104-6, ISSN:1539-3755 DOI Accesso ONLINE all'editore

Marsili, Simone; Chelli, Riccardo; Schettino, Vincenzo; Procacci, Piero (2008). Thermodynamics of stacking interactions in proteins. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, pp. 2673-2685, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Marsili, Simone; Barducci, Alessandro; Procacci, Piero (2007). Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations. THE JOURNAL OF CHEMICAL PHYSICS, vol. 127, pp. 034110-1-034110-9, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Schettino, Vincenzo; Chelli, Riccardo; Marsili, Simone; Barducci, Alessandro; Faralli, Cristian; Pagliai, Marco; Procacci, Piero; Cardini, Gianni (2007). Problems in molecular dynamics of condensed phases. THEORETICAL CHEMISTRY ACCOUNTS, vol. 117, pp. 1105-1120, ISSN:1432-881X DOI Accesso ONLINE all'editore

Chelli, Riccardo; Marsili, Simone; Barducci, Alessandro; Procacci, Piero (2007). Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: A strategy based on the equations of motion. THE JOURNAL OF CHEMICAL PHYSICS, vol. 126, pp. 044502-1-044502-7, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Piquemal, Jean-Philip; Chelli, Riccardo; Procacci, Piero; Gresh, Nohad (2007). Key role of the polarization anisotropy of water in modeling classical polarizable force fields. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 111, pp. 8170-8176, ISSN:1089-5639 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Marsili, Simone; Barducci, Alessandro; Procacci, Piero (2007). Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations. PHYSICAL REVIEW E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS, vol. 75, pp. 050101-1-050101-4, ISSN:1539-3755 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Procacci, Piero (2006). Comment on “From Subtle to Substantial: Role of Metal Ions on π−π Interactions”. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 110, pp. 10204-10205, ISSN:1520-6106 DOI Accesso ONLINE all'editore

Procacci, Piero; Marsili, Simone; Barducci, Alessandro; Signorini, F. Giorgio; Chelli, Riccardo (2006). Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat. THE JOURNAL OF CHEMICAL PHYSICS, vol. 125, pp. 164101-1-164101-9, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Barducci, Alessandro; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo; Gervasio, L. Francesco; Parrinello, Michele (2006). Metadynamics simulation of prion protein: β-structure stability and the early stages of misfolding. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 128, pp. 2705-2710, ISSN:0002-7863 DOI Accesso ONLINE all'editore

Marsili, Simone; Barducci, Alessandro; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo (2006). Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 110, pp. 14011-14013, ISSN:1520-6106 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Pagliai, Marco; Procacci, Piero; Cardini, Gianni; Schettino, Vincenzo (2005). Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: Implications for charge transfer. THE JOURNAL OF CHEMICAL PHYSICS, vol. 122, pp. 074504-1-074504-10, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Barducci, Alessandro; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo (2005). Misfolding pathways of the prion protein probed by molecular dynamics simulations. BIOPHYSICAL JOURNAL, vol. 88, pp. 1334-1343, ISSN:0006-3495 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Barducci, Alessandro; Bellucci, Luca; Schettino, Vincenzo; Procacci, Piero (2005). Behavior of polarizable models in presence of strong electric fields. I. Origin of nonlinear effects in water point-charge systems. THE JOURNAL OF CHEMICAL PHYSICS, vol. 123, pp. 194109-1-194109-8, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Schettino, Vincenzo; Procacci, Piero (2005). Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases. THE JOURNAL OF CHEMICAL PHYSICS, vol. 122, pp. 234107-1-234107-7, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Procacci, Piero (2004). Comment to “Calculation of the Dipole Moment for Polypeptides Using the Generalized Born-Electronegativity Equalization Method: Results in Vacuum and Continuum-Dielectric Solvent”. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 108, pp. 16995-16997, ISSN:1520-6106 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Gervasio, L. Francesco; Procacci, Piero; Schettino, Vincenzo (2004). Inter-residue and solvent-residue interactions in proteins: A statistical study on experimental structures. PROTEINS, vol. 55, pp. 139-151, ISSN:0887-3585 DOI Accesso ONLINE all'editore

Signorini F. Giorgio; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo (2004). Energetic fitness of histidine protonation states in PDB structures. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 108, pp. 12252-12257, ISSN:1520-6106 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Procacci, Piero (2003). Comment on "Classical polarizable force fields parametrized from ab initio calculations" [J. Chem. Phys. 117, 1416 (2002)]. THE JOURNAL OF CHEMICAL PHYSICS, vol. 118, pp. 1571-1572, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Cardini, Gianni; Procacci, Piero; Righini, Roberto; Califano, Salvatore (2003). Dynamical and structural correlation in supercooled liquids: a molecular dynamics investigation of m-toluidine. THE JOURNAL OF CHEMICAL PHYSICS, vol. 119, pp. 357-363, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Cardini, Gianni; Procacci, Piero; Righini, Roberto; Califano, Salvatore (2003). Dynamics and structure of liquid and supercooled liquid m-toluidine investigated by molecular dynamics simulations. In: XII UPS Conference: Recent Advances in Ultrafast Spectroscopy, Firenze, Ottobre 2001, Leo S. Olschki, Firenze, pp. 57-67, ISBN:8822252519

MATTEO CECCARELLI; P. PROCACCI; MASSIMO MARCHI (2003). Force Field for the Cofactors of Bacterial Photosynthesis. JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 24, pp. 129-142, ISSN:0192-8651, John Wiley & Sons Incorporated:Customer Service, 111 River Street:Hoboken, NJ 07030:(800)225-5945, (201)748-6000, EMAIL: societyinfo@wiley.com, INTERNET: http://www.wiley.com, Fax: (212)748-6551:

Chelli, Riccardo; Cardini, Gianni; Procacci, Piero; Righini, Roberto; Califano, Salvatore (2002). Molecular dynamics of glass-forming liquids: Structure and dynamics of liquid metatoluidine. THE JOURNAL OF CHEMICAL PHYSICS, vol. 116, pp. 6205-6215, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Procacci, Piero (2002). A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle. THE JOURNAL OF CHEMICAL PHYSICS, vol. 117, pp. 9175-9189, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Gervasio, L. Francesco; Procacci, Piero; Schettino, Vincenzo (2002). Stacking and T-shape competition in aromatic−aromatic amino acid interactions. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 124, pp. 6133-6143, ISSN:0002-7863 DOI Accesso ONLINE all'editore

Gervasio, L. Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo (2002). The nature of intermolecular interactions between aromatic amino acid residues. PROTEINS, vol. 48, pp. 117-125, ISSN:0887-3585 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Righini, Roberto; Califano, Salvatore; Procacci, Piero (2002). Towards a polarizable force field for molecular liquids. JOURNAL OF MOLECULAR LIQUIDS, vol. 96-97, pp. 87-100, ISSN:0167-7322 DOI Accesso ONLINE all'editore

Gervasio, L. Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo (2002). Is the T-shaped toluene dimer a stable intermolecular complex?. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 106, pp. 2945-2948, ISSN:1089-5639 DOI Accesso ONLINE all'editore

Matteo Ceccarelli;Piero Procacci;Massimo Marchi (2001). Empirical force field for the simulation of a class of chromophores in a photosynthetic center. COMPUTATIONAL MATERIALS SCIENCE, vol. 20, pp. 318-324, ISSN:0927-0256 DOI

Gervasio, L. Francesco; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero; Schettino, Vincenzo (2001). 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. JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL, vol. 105, pp. 7835-7846, ISSN:1520-6106 DOI Accesso ONLINE all'editore

M. Marchi;P. Procacci (2001). Comment on “Efficient stress relaxation in molecular dynamics simulations of semiflexible n-alkanes” [Phys. Rev. E. 58, 6766 (1998)]. PHYSICAL REVIEW E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS, vol. 63, pp. 0280701-0280701-3, ISSN:1539-3755 DOI Accesso ONLINE all'editore

FRANCESCO LUIGI GERVASIO; PIERO PROCACCI; GIANNI CARDINI; ANTONIO GUARNA; ALESSANDRO GIOLITTI; V. SCHETTINO (2000). Interaction between aromatic residues. Molecular dynamics and ab initio exploration of the potential energy surface of the tryptophan-histidine pair. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 104, pp. 1108-1114, ISSN:1089-5639 DOI

Piero Procacci; Massimo Marchi (2000). Multiple time steps algorithms for the atomistic simulations of complex molecular systems. In: P. Pasini, C. Zannoni. ADVANCES IN THE COMPUTER SIMULATIONS OF LIQUID CRYSTALS, pp. 333-387, Dordrecht: Kluwer Academic Publishers, ISBN:0792360982. Accesso ONLINE all'editore

Chelli, Riccardo; Gervasio, L. Francesco; Gellini, Cristina; Procacci, Piero; Cardini, Gianni; Schettino, Vincenzo (2000). Conformational distribution of gas-phase glycerol. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 104, pp. 11220-11222, ISSN:1089-5639 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Ciabatti, Sonia; Cardini, Gianni; Righini, Roberto; Procacci, Piero (2000). Erratum: “Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method” [J. Chem. Phys. 111, 4218 (1999)]. THE JOURNAL OF CHEMICAL PHYSICS, vol. 112, pp. 5515-5515, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Cardini, Gianni; Procacci, Piero; Righini, Roberto; Califano, Salvatore; Albrecht, Andreas (2000). Simulated structure, dynamics and vibrational spectra of liquid benzene. THE JOURNAL OF CHEMICAL PHYSICS, vol. 113, pp. 6851-6863, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Gervasio, L. Francesco; Gellini, Cristina; Procacci, Piero; Cardini, Gianni; Schettino, Vincenzo (2000). Density functional calculation of structural and vibrational properties of glycerol. JOURNAL OF PHYSICAL CHEMISTRY. A, MOLECULES, SPECTROSCOPY, KINETICS, ENVIRONMENT, & GENERAL THEORY, vol. 104, pp. 5351-5357, ISSN:1089-5639 DOI Accesso ONLINE all'editore

R.G Della Valle;P Procacci (2000). Computer-Aided Series Expansion for Phonon Self-Energy. JOURNAL OF COMPUTATIONAL PHYSICS, vol. 165, pp. 428-436, ISSN:0021-9991 DOI

Chelli, Riccardo; Procacci, Piero; Righini, Roberto; Califano, Salvatore (1999). Electrical response in chemical potential equalization schemes. THE JOURNAL OF CHEMICAL PHYSICS, vol. 111, pp. 8569-8575, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Procacci, Piero; Cardini, Gianni; Della Valle, G. Raffaele; Califano, Salvatore (1999). Glycerol condensed phases Part I. A molecular dynamics study. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 1, pp. 871-877, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Chelli, Riccardo; Procacci, Piero; Cardini, Gianni; Califano, Salvatore (1999). Glycerol condensed phases part II. A molecular dynamics study of the conformational structure and hydrogen bonding. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 1, pp. 879-885, ISSN:1463-9076 DOI Accesso ONLINE all'editore

Chelli Riccardo; Ciabatti, Sonia; Cardini, Gianni; Righini, Roberto; Procacci, Piero (1999). Calculation of optical spectra in liquid methanol using molecular dynamics and the chemical potential equalization method. THE JOURNAL OF CHEMICAL PHYSICS, vol. 111, pp. 4218-4229, ISSN:0021-9606 DOI Accesso ONLINE all'editore

Piero Procacci;Massimo Marchi;Glenn J. Martyna (1998). Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems. THE JOURNAL OF CHEMICAL PHYSICS, vol. 108, pp. 8799-8803, ISSN:0021-9606 DOI Accesso ONLINE all'editore

P. Procacci; M. Souaille (1998). Modeling the solvent effect in electronic transitions. In: Bruce J. Berne, Giovanni Ciccotti, David F. Coker.. Classical and quantum dynamics in condensed phased simulations : proceedings of the International School of Physics "Computer Simulation of Rare Events and Dynamics of Classical and Quantum Condensed-Phased Systems" : Lerici, Villa Marigola, 7 July-18 July 1997, pp. 759-778, Singapore: World Scientific (Singapore, New Jersey, London, Hong Kong), ISBN:9789810234980.

Massimo Marchi;Piero Procacci (1998). Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble. THE JOURNAL OF CHEMICAL PHYSICS, vol. 109, pp. 5194-5202, ISSN:0021-9606 DOI

P. PROCACCI; PACI E.; T. DARDEN; M. MARCHI (1997). ORAC: A Molecular Dynamics Program to Simulate Complex Molecular Systems with Realistic Electrostatic Interactions. JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 18, pp. 1848-1862, ISSN:0192-8651, John Wiley & Sons Incorporated:Customer Service, 111 River Street:Hoboken, NJ 07030:(800)225-5945, (201)748-6000, EMAIL: societyinfo@wiley.com, INTERNET: http://www.wiley.com, Fax: (212)748-6551:

R. G. Della Valle;G. F. Signorini;P. Procacci (1997). Vibrational density of states and homogeneous linewidth in molecular crystals: Many-phonon processes in nitrogen. PHYSICAL REVIEW. B, CONDENSED MATTER, vol. 55, pp. 14855-14864, ISSN:0163-1829 DOI

P. Procacci; M. Marchi (1997). Orac 5 User Manual, Release 5.3: A Molecular Dynamics Program to Simulate Complex Molecular System at the atomistic level. pp. 1-170 Accesso ONLINE all'editore

Piero Procacci;Massimo Marchi (1996). Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm. THE JOURNAL OF CHEMICAL PHYSICS, vol. 104, pp. 3003-3012, ISSN:0021-9606 DOI

Piero Procacci;Tom Darden;Massimo Marchi (1996). A Very Fast Molecular Dynamics Method To Simulate Biomolecular Systems with Realistic Electrostatic Interactions. THE JOURNAL OF PHYSICAL CHEMISTRY, vol. 100, pp. 10464-10468, ISSN:0022-3654 DOI

Piero Procacci;B.J. Berne (1994). Multiple time scale methods for constant pressure molecular dynamics simulations of molecular systems. MOLECULAR PHYSICS, vol. 83, pp. 255-272, ISSN:0026-8976 DOI

Piero Procacci;B. J. Berne (1994). Computer simulation of solid C60 using multiple time-step algorithms. THE JOURNAL OF CHEMICAL PHYSICS, vol. 101, pp. 2421-2431, ISSN:0021-9606 DOI

Piero Procacci;Giorgio Signorini;Raffaele Della Valle (1993). Efficient calculation of high-order self-energy corrections to phonon linewidths: Application to α-nitrogen. PHYSICAL REVIEW. B, CONDENSED MATTER, vol. 47, pp. 11124-11133, ISSN:0163-1829 DOI

Procacci, P.; Cardini, G.; Salvi, P.R. (1993). A vibrational potential function for molecular dynamics simulation of buckminsterfullerene. MOLECULAR CRYSTALS AND LIQUID CRYSTALS SCIENCE AND TECHNOLOGY. SECTION A, MOLECULAR CRYSTALS AND LIQUID CRYSTALS, vol. 229, pp. 75-81, ISSN:1058-725X DOI Accesso ONLINE all'editore

G.Cardini;P.Procacci;P.Salvi;V.Schettino (1993). Molecular dynamics simulation of rare gas fullerene adducts. LOW TEMPERATURE PHYSICS, vol. 19, pp. 562-566, ISSN:1063-777X

G.Marconi;P.Salvi;P.Procacci (1993). Vibronic interactions in the lowest excited singlet state of C60. JOURNAL OF MOLECULAR STRUCTURE, vol. 294, pp. 57-60, ISSN:0022-2860

R.Bini;P.Procacci;P.Salvi;V.Schettino (1993). The far infrared spectrum of C60. THE JOURNAL OF PHYSICAL CHEMISTRY, vol. 97, pp. 10580-10584, ISSN:0022-3654

Raffaele Della Valle;Piero Procacci (1992). Equation of motion for the Green’s function in anharmonic solids. PHYSICAL REVIEW. B, CONDENSED MATTER, vol. 46, pp. 6141-6149, ISSN:0163-1829 DOI

P. PROCACCI; G. CARDINI; PR. SALVI; V. SCHETTINO (1992). Vibrational frequencies of C70. CHEMICAL PHYSICS LETTERS, vol. 195, pp. 347-351, ISSN:0009-2614

Piero Procacci;Riccardo Scateni (1992). A general algorithm for computing Voronoi volumes: Application to the hydrated crystal of myoglobin. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, vol. 42, pp. 1515-1528, ISSN:0020-7608 DOI

P. PROCACCI; G. CARDINI; R. RIGHINI; S. CALIFANO (1992). Anharmonic lattice dynamics and computer simulation for simple model systems. PHYSICAL REVIEW. B, CONDENSED MATTER, vol. 45, pp. 2113-2125, ISSN:0163-1829, American Institute of Physics:2 Huntington Quadrangle, Suite 1NO1:Melville, NY 11747:(800)344-6902, (631)576-2287, EMAIL: subs@aip.org, INTERNET: http://www.aip.org, Fax: (516)349-9704:

G. CARDINI; P. PROCACCI; P. R. SALVI; V. SCHETTINO (1992). Vibrational properties of Xe-fullerenes adducts: a Molecular Dynamics approach. CHEMICAL PHYSICS LETTERS, vol. 200, pp. 39-45, ISSN:0009-2614, Elsevier BV:PO Box 211, 1000 AE Amsterdam Netherlands:011 31 20 4853757, 011 31 20 4853642, 011 31 20 4853641, EMAIL: nlinfo-f@elsevier.nl, INTERNET: http://www.elsevier.nl, Fax: 011 31 20 4853598:

E. Clementi; S. Chin; G. Corongiu; J. Given; G. C. Lie; M. Migliore; P. Procacci (1991). Supercomputer Simulations of the Interactions of Biomolecules. In: AA VV. Interfacial Phenomena in Biological Systems (Surfactant Science), pp. 301-333, New York: Marcel Dekker Inc., ISBN:9780824784362.

P.Procacci;A.Tafi;L.Angeloni;R.Righini;P.Salvi (1991). Vibrational relaxation in crystal SO2. CHEMICAL PHYSICS, vol. 154, pp. 331-342, ISSN:0301-0104

A.Tafi;P.Procacci;E.Castellucci;P.Salvi (1991). Polar phonons in SO2 single crystal. CHEMICAL PHYSICS, vol. 150, pp. 205-217, ISSN:0301-0104

P. Procacci; D. M. Soumpasis; G. Corongiu (1991). IBM DSD Report: Part B: Triplet Correlations in NCC water. pp. 16-43

P. Procacci; G. Corongiu; E. Clementi (1989). IBM DSD Report: Structure and Dynamics of Water in the Crystal of Myoglobin. pp. 1-32

P. Procacci; G. Corongiu; E. Clementi (1989). IBM DSD Report: Ewald Procedure in Molecular Dynamics Simulations of Pure Liquids and Solutions. pp. 1-46

E. Clementi; G. Corongiu; G.C. Lie; U. Niesar; P. Procacci (1989). Monte Carlo and Molecular Dynamics Simulations. In: Enrico Clementi. Modern Techniques in Computational Chemistry: MOTECC-89, pp. 363-424, Leiden: ESCOM, ISBN:9072199057.

Gianni Cardini;Piero Procacci;Roberto Righini (1987). Molecular dynamics and anharmonic effects in the phonon spectra of solid carbon dioxide. CHEMICAL PHYSICS, vol. 117, pp. 355-366, ISSN:0301-0104 DOI

Piero Procacci;Roberto Righini;Salvatore Califano (1987). Anharmonic calculation of bandwidths and frequency shifts in crystalline CO2. CHEMICAL PHYSICS, vol. 116, pp. 171-186, ISSN:0301-0104 DOI

Piero PROCACCI

Curriculum

PIERO PROCACCI, Ph. D. in Chemistry
Associate Professor of Physical-Chemistry, University of Florence

PERSONAL DETAILS

- Family Name: Procacci
- Name: Piero
- Sex: Male
- Born: 23rd January 1961
- Citizenship: Italian
- Address: Chemistry Dept., University of Florence, Via Lastruccia n. 3, Sesto F.no
- Phone: 055-4573081
- Email: procacci@unifi.it

EDUCATION AND QUALIFICATIONS

- 1974 - 1979: Italian Secondary School (classic studies)
- 1979: "Liceo Classico" Secondary School Degree (Diploma)
- 1980 - 1986: School of Chemistry, University of Florence
- 1986: Master in Chemistry (Italian "Laurea), Florence University
- 1989 -1993 Ph. D. Studentship in Chemistry, Dept. of Chemistry, University of Florence
- 1993: Ph. D. Degree in Chemistry, University of Florence

GRANTS (as a PI) AND AWARDS

- February 1993: Consiglio Delle Ricerche National Fellowship Grant in Physical-Chemistry (38/50 points)
- March 1996: Training and Mobility Grant n. FMBI950363 for the Project: Electronic transitions in the photosynthetic reaction center
- September 2001: Qualification for Assistant Professorship (Bando Nazionale)
- April 2004: Qualification for Associate Professorship, Physical-Chemistry, University of Florence
- October 2009: Regione Toscana 2yrs Grant for the Project, "In silico Assessment of peptides with potential pharmaceutical properties for Multiple Sclerosis."
- June 2011: CINECA-ISCRA-B Grant HP10BDV7I7-FKBP12-L for the project: "Determining the binding affinities for drug receptor complexes at the full atomistic level using solute tempering and multiple Bennett acceptance ratio : the case of FKBP12 tacrolimous related ligands"
- January 2014: Qualification for full Professorship, Scientific Sector 03/A2, Physical Chemistry (Abilitazione Scientifica Nazionale Prima Fascia)
- June 2015: CINECA-ISCRA-C Grant HP10CSNWHM- MPNEDRUG for the Project "An Hybrid MPI and OpenMP parallel non-equilibrium method for fast calculations of the binding free energy in Molecular Dynamics Simulations of ligand-receptor systems"
- July 2016: CINECA-ISCRA-B Grant INHITACE - HP10BH62LR for the Project "Design of new small inhibitors for the tumor necrosis factor-alpha converting enzyme: a possible route for controlling the inflammatory response in autoimmune diseases."
- January 2017: Qualification for full Professorship, Scientific Sector 02/B2, Theoretical Physics of the Condensed Matter (Abilitazione Scientifica Nazionale Prima Fascia)
- October 2017 Partnership for Advance Computing in Europe (PRACE), 17,000,000 of core hours on Tier-0 platforms for the Projects "Drug design for HPC systems: Fast Switching Double Annihilation Method (FS-DAM) at work" www.prace-ri.eu
- December 2017 CINECA-ISCRA-C Grant F-SAMPL6-HP10CG5AD "Fast swicthing double annihilation in the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL6) challenge"

EMPLOYMENTS

- Jan 1988 -Aug 1989: Associate Researcher (Prof. Enrico Clementi's group),Department of Scientific and Engineering Computations, IBM corporation, Kingston NY (USA),
- July 1993 - June 1994: PostDoctoral Fellow, Department of Chemistry, Columbia University (Prof. Bruce J. Berne's group), New York NY (USA)
- October 1994 - December 1996: PostDoctoral Fellow, Centre Europeen de Calcul Atomic et Moleculaire (CECAM), Ecole Normale Superieure, Lyon (FRANCE)
- January 1997 - Sept 2001: Associate researcher, Department of Chemistry, University of Florence
- Sept 2001-May 2005: Assistant Professor, Department of Chemistry, University of Florence
- May 2005 - Today : Associate Professor in Chemical Physics, University of Florence

REVIEWING ASSIGNMENTS

- Journal of the American Chemical Society
- Physical Chemistry Chemical Physics
- Journal of Chemical Physics
- Journal of Physical Chemistry
- Chemical Physics
- Physical Review Letters
- Referee for the ERC Consolidator Grant 2013, ERC Sectors PE4_13, PE4_15, LS7_3)
- Referee for The Partnership for Advanced Computing in Europe (PRACE), ERC Sectors PE4_13, PE4_15, LS7_3
- Referee for Italian Super-Computing Resource Allocation (ISCRA)
- Referee for Italian Bando FIRB, (PE4_13, PE4_15 ERC-based sectors)

SCIENTIFIC COLLABORATIONS

- European Laboratory of non Linear Spectroscopy (LENS), Florence
- Department of Physics, University of Florence
- Dipartimento di Neuroscienze, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence
- Sviluppo Sistemi per l'informatica e l'ITC della Agenzia nazionale Nuove Tecnologie (ENEA)
- Laboratoire bioénergétique membranaire et stress (LBMS), Centre D'Etudes, CEA Sacly Gif Sur Yvette (France)
- Department of Chemistry and Applied Biosciences, ETH Zurich (Switzerland), Prof. Michele Parrinello's Group
- Centre Europeen de Calcul Atomic et Moleculaire (CECAM), Ecole Normale Superieure, Lyon (FRANCE)

MAIN RESEARCH FIELDS (ERC-based):

- PE3_17 Statistical physics (condensed matter)
- PE4_13 Physical chemistry of biological systems
- PE4_15 Theoretical and computational chemistry
- LS2_14 Biological systems analysis, modeling and simulation
- LS7_3 Pharmacology, pharmacogenomics, drug discovery and design, drug therapy

RESEARCH ACTIVITY AND RELATED BIBLIOMETRIC DATA

- co-author or author of 95 Publications on peer-reviewed Journal indexed by the ISI/SCOPUS Databases.
- co-author of 11 contributions (Book Chapter) in Scientific Collections/Books.
- Last 5 years publications: 21 Articles on Peer Reviewed Journals and 4 Book Chapters
- Release of ORAC3.0, "ORAC: A Molecular Dynamics Program to Simulate
Complex Molecular Systems with Realistic Electrostatic Interactions" (J Comp Chem 1997)
- Release of ORAC5.0 for MPI (Message Passing Interface) platforms, "ORAC: A molecular dynamics
simulation program to explore free energy surfaces in bio-molecular systems at the atomistic
level." (J Comp Chem 1997, Software News and Update)
- Release of the hybrid OpenMP/MPI code ORAC6.0 for NUMA (non uniform access memory) HPC platforms,
"Hybrid mpi/openmp implementation of the orac molecular dynamics program for generalized
ensemble and fast switching alchemical simulations", P Procacci www.chim.unifi.it/orac
Journal of chemical information and modeling 56 (6), 1117-1121
- Google Scholar Total Citations 3207 (h-index 33)
- Scopus Total Citation 2432 (h-index 30)