Piero Procacci

Affiliations

University of Florence, Department of Chemistry, Via Lastruccia n. 3, 50019, Sesto Fiorentino, FI, Italy. procacci@unifi.it.

ORCID: 0000-0003-2667-3847

Publications (47)

SAMPL7 blind predictions using nonequilibrium alchemical approaches.

Journal of computer-aided molecular design

Avec: Piero Procacci , Guido Guarnieri

Mitochondrial functional and structural impairment is involved in the antitumor activity of δ-tocotrienol in prostate cancer cells.

Free radical biology & medicine

Avec: Fabrizio Fontana , Michela Raimondi , Monica Marzagalli , Matteo Audano , Giangiacomo Beretta , Patrizia Procacci , Patrizia Sartori , Nico Mitro , Patrizia Limonta

Identification of potential binders of the main protease 3CL

Chemical physics letters

Avec: Marina Macchiagodena , Marco Pagliai , Piero Procacci

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

ACS omega

Avec: Marina Macchiagodena , Marco Pagliai , Claudia Andreini , Antonio Rosato , Piero Procacci

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

The Journal of chemical physics

Avec: Piero Procacci , Guido Guarnieri

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

Avec: Marina Macchiagodena , Marco Pagliai , Claudia Andreini , Antonio Rosato , Piero Procacci

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

The Journal of chemical physics

Avec: Piero Procacci

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

Avec: Gabriella Caminati , Maria Raffaella Martina , Stefano Menichetti , Piero Procacci

Characterization of an in vitro model to study the possible role of polyomavirus BK in prostate cancer.

Journal of cellular physiology

Avec: Sonia Villani , Nicoletta Gagliano , Patrizia Procacci , Patrizia Sartori , Manola Comar , Maurizio Provenzano , Evaldo Favi , Mariano Ferraresso , Pasquale Ferrante , Serena Delbue

The Antagonism of the Prokineticin System Counteracts Bortezomib Induced Side Effects: Focus on Mood Alterations.

International journal of molecular sciences

Avec: Giada Amodeo , Benedetta Verduci , Patrizia Sartori , Patrizia Procacci , Vincenzo Conte , Gianfranco Balboni , Paola Sacerdote , Silvia Franchi

Activity of Experimental Mouthwashes and Gels Containing DNA-RNA and Bioactive Molecules against the Oxidative Stress of Oral Soft Tissues: The Importance of Formulations. A Bioreactor-Based Reconstituted Human Oral Epithelium Model.

Molecules (Basel, Switzerland)

Avec: Andrei C Ionescu , Elena Vezzoli , Vincenzo Conte , Patrizia Sartori , Patrizia Procacci , Eugenio Brambilla

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

Journal of chemical theory and computation

Avec: Piero Procacci

Persistent Idiopathic Facial Pain (PIFP) in Patients Referred to a Multidisciplinary Centre in Italy: A Retrospective Observational Study.

Journal of clinical medicine

Avec: Vittorio Schweiger , Riccardo Nocini , Daniele De Santis , Pasquale Procacci , Giovanni Zanette , Erica Secchettin , Giovanna Del Balzo , Andrea Fior , Alvise Martini , Marta Nizzero , Katia Donadello , Gabriele Finco , Leonardo Gottin , Enrico Polati

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

Chemical communications (Cambridge, England)

Avec: Piero Procacci , Marina Macchiagodena , Marco Pagliai , Guido Guarnieri , Francesco Iannone

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

Physical chemistry chemical physics : PCCP

Avec: Piero Procacci

Is post orthognathic maxillary sinusitis related to sino-nasal anatomical alterations?

Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery

Avec: Pasquale Procacci , Luca Lanaro , Lorenzo Trevisiol , Dario Bertossi , Francesca Zotti , Lonardi Fabio , Antonio D'Agostino

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

Avec: Marina Macchiagodena , Marco Pagliai , Maurice Karrenbrock , Guido Guarnieri , Francesco Iannone , Piero Procacci

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Apoptosis : an international journal on programmed cell death

Avec: Michela Raimondi , Fabrizio Fontana , Monica Marzagalli , Matteo Audano , Giangiacomo Beretta , Patrizia Procacci , Patrizia Sartori , Nico Mitro , Patrizia Limonta

Simvastatin Prevents Liver Microthrombosis and Sepsis Induced Coagulopathy in a Rat Model of Endotoxemia.

Cells

Avec: Vincenzo La Mura , Nicoletta Gagliano , Francesca Arnaboldi , Patrizia Sartori , Patrizia Procacci , Luca Denti , Eleonora Liguori , Niccolò Bitto , Giuseppe Ristagno , Roberto Latini , Daniele Dondossola , Francesco Salerno , Armando Tripodi , Massimo Colombo , Flora Peyvandi

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

Journal of chemical theory and computation

Avec: Piero Procacci

Adipocyte-Derived Extracellular Vesicles Promote Prostate Cancer Cell Aggressiveness by Enabling Multiple Phenotypic and Metabolic Changes.

Cells

Avec: Fabrizio Fontana , Martina Anselmi , Emanuela Carollo , Patrizia Sartori , Patrizia Procacci , David Carter , Patrizia Limonta

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

Avec: Marina Macchiagodena , Marco Pagliai , Piero Procacci

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

The journal of physical chemistry. A

Avec: Marina Macchiagodena , Gavino Bassu , Irene Vettori , Emiliano Fratini , Piero Procacci , Marco Pagliai

Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations.

The journal of physical chemistry. B

Avec: Maurice Karrenbrock , Valerio Rizzi , Piero Procacci , Francesco Luigi Gervasio

Acid Sphingomyelinase Downregulation Enhances Mitochondrial Fusion and Promotes Oxidative Metabolism in a Mouse Model of Melanoma.

Cells

Avec: Marco Coazzoli , Alessandra Napoli , Paulina Roux-Biejat , Clara De Palma , Claudia Moscheni , Elisabetta Catalani , Silvia Zecchini , Vincenzo Conte , Matteo Giovarelli , Sonia Caccia , Patrizia Procacci , Davide Cervia , Emilio Clementi , Cristiana Perrotta

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

Journal of computer-aided molecular design

Avec: Piero Procacci

δ-Tocotrienol induces apoptosis, involving endoplasmic reticulum stress and autophagy, and paraptosis in prostate cancer cells.

Cell proliferation

Avec: Fabrizio Fontana , Roberta Manuela Moretti , Michela Raimondi , Monica Marzagalli , Giangiacomo Beretta , Patrizia Procacci , Patrizia Sartori , Marina Montagnani Marelli , Patrizia Limonta

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

Avec: Dario Vassetti , Marco Pagliai , Piero Procacci

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

The journal of physical chemistry. B

Avec: Marco Pagliai , Giada Funghi , Dario Vassetti , Piero Procacci , Riccardo Chelli , Gianni Cardini

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

Journal of computer-aided molecular design

Avec: Piero Procacci , Marina Macchiagodena

Effects of Na-DNA mouthwash solutions on oral soft tissues. A bioreactor-based reconstituted human oral epithelium model.

American journal of dentistry

Avec: Andrei C Ionescu , Elena Vezzoli , Vicenzo Conte , Patrizia Procacci , Franklin Garcia-Godoy , Eugenio Brambilla

Pre-Drawn Syringes of Comirnaty for an Efficient COVID-19 Mass Vaccination: Demonstration of Stability.

Pharmaceutics

Avec: Francesca Selmin , Umberto M Musazzi , Silvia Franzè , Edoardo Scarpa , Loris Rizzello , Patrizia Procacci , Paola Minghetti

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

Molecules (Basel, Switzerland)

Avec: 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

Avec: Giorgio Di Paco , Marina Macchiagodena , Piero Procacci

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

The Journal of chemical physics

Avec: Piero Procacci

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

Journal of computer-aided molecular design

Avec: Piero Procacci , Guido Guarnieri

Targeting prokineticin system counteracts hypersensitivity, neuroinflammation, and tissue damage in a mouse model of bortezomib-induced peripheral neuropathy.

Journal of neuroinflammation

Avec: Giorgia Moschetti , Giada Amodeo , Daniela Maftei , Roberta Lattanzi , Patrizia Procacci , Patrizia Sartori , Gianfranco Balboni , Valentina Onnis , Vincenzo Conte , Alberto Panerai , Paola Sacerdote , Silvia Franchi

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

Avec: Marco Pagliai , Marina Macchiagodena , Piero Procacci , Gianni Cardini

Mounting evidence of FKBP12 implication in neurodegeneration.

Neural regeneration research

Avec: Gabriella Caminati , Piero Procacci

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

Journal of molecular graphics & modelling

Avec: Marina Macchiagodena , Marco Pagliai , Piero Procacci

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

Journal of chemical information and modeling

Avec: Marina Macchiagodena , Maurice Karrenbrock , Marco Pagliai , Piero Procacci

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

Bioelectrochemistry (Amsterdam, Netherlands)

Avec: Hasret Subak , Giulia Selvolini , Marina Macchiagodena , Dilsat Ozkan-Ariksoysal , Marco Pagliai , Piero Procacci , Giovanna Marrazza

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

Current opinion in structural biology

Avec: 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

Avec: Lorenzo Casbarra , Piero Procacci

SAMPL9 blind predictions using nonequilibrium alchemical approaches.

The Journal of chemical physics

Avec: Piero Procacci , Guido Guarnieri

Caffeic Acid-Grafted PLGA as a Novel Material for the Design of Fluvastatin-Eluting Nanoparticles for the Prevention of Neointimal Hyperplasia.

Molecular pharmaceutics

Avec: Stefano Bellosta , Francesca Selmin , Giulia Magri , Silvia Castiglioni , Patrizia Procacci , Patrizia Sartori , Edoardo Scarpa , Valerio Tolva , Clara Rossi , Francesco Puoci , Loris Rizzello , Francesco Cilurzo

Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems.

Physical chemistry chemical physics : PCCP

Avec: Zhaoxi Sun , Piero Procacci

Réseau de co-auteurs

Patrizia Procacci 13 collaborations

Marina Macchiagodena 13 collaborations

Marco Pagliai 13 collaborations

Patrizia Sartori 10 collaborations

Guido Guarnieri 6 collaborations

Fabrizio Fontana 4 collaborations

Patrizia Limonta 4 collaborations

Vincenzo Conte 4 collaborations

Michela Raimondi 3 collaborations

Monica Marzagalli 3 collaborations

Giangiacomo Beretta 3 collaborations

Maurice Karrenbrock 3 collaborations

Matteo Audano 2 collaborations

Nico Mitro 2 collaborations

Claudia Andreini 2 collaborations

Antonio Rosato 2 collaborations

Gabriella Caminati 2 collaborations

Nicoletta Gagliano 2 collaborations

Giada Amodeo 2 collaborations

Gianfranco Balboni 2 collaborations

Paola Sacerdote 2 collaborations

Silvia Franchi 2 collaborations

Andrei C Ionescu 2 collaborations

Elena Vezzoli 2 collaborations

Eugenio Brambilla 2 collaborations

Pasquale Procacci 2 collaborations

Francesco Iannone 2 collaborations

Dario Vassetti 2 collaborations

Gianni Cardini 2 collaborations

Francesca Selmin 2 collaborations

Edoardo Scarpa 2 collaborations

Loris Rizzello 2 collaborations

Maria Raffaella Martina 1 collaboration

Stefano Menichetti 1 collaboration

Sonia Villani 1 collaboration

Manola Comar 1 collaboration

Maurizio Provenzano 1 collaboration

Evaldo Favi 1 collaboration

Mariano Ferraresso 1 collaboration

Pasquale Ferrante 1 collaboration

Serena Delbue 1 collaboration

Benedetta Verduci 1 collaboration

Vittorio Schweiger 1 collaboration

Riccardo Nocini 1 collaboration

Daniele De Santis 1 collaboration

Giovanni Zanette 1 collaboration

Erica Secchettin 1 collaboration

Giovanna Del Balzo 1 collaboration

Andrea Fior 1 collaboration

Alvise Martini 1 collaboration

Marta Nizzero 1 collaboration

Katia Donadello 1 collaboration

Gabriele Finco 1 collaboration

Leonardo Gottin 1 collaboration

Enrico Polati 1 collaboration

Luca Lanaro 1 collaboration

Lorenzo Trevisiol 1 collaboration

Dario Bertossi 1 collaboration

Francesca Zotti 1 collaboration

Lonardi Fabio 1 collaboration

Antonio D'Agostino 1 collaboration

Vincenzo La Mura 1 collaboration

Francesca Arnaboldi 1 collaboration

Luca Denti 1 collaboration

Eleonora Liguori 1 collaboration

Niccolò Bitto 1 collaboration

Giuseppe Ristagno 1 collaboration

Roberto Latini 1 collaboration

Daniele Dondossola 1 collaboration

Francesco Salerno 1 collaboration

Armando Tripodi 1 collaboration

Massimo Colombo 1 collaboration

Flora Peyvandi 1 collaboration

Martina Anselmi 1 collaboration

Emanuela Carollo 1 collaboration

David Carter 1 collaboration

Gavino Bassu 1 collaboration

Irene Vettori 1 collaboration

Emiliano Fratini 1 collaboration

Valerio Rizzi 1 collaboration

Francesco Luigi Gervasio 1 collaboration

Marco Coazzoli 1 collaboration

Alessandra Napoli 1 collaboration

Paulina Roux-Biejat 1 collaboration

Clara De Palma 1 collaboration

Claudia Moscheni 1 collaboration

Elisabetta Catalani 1 collaboration

Silvia Zecchini 1 collaboration

Matteo Giovarelli 1 collaboration

Sonia Caccia 1 collaboration

Davide Cervia 1 collaboration

Emilio Clementi 1 collaboration

Cristiana Perrotta 1 collaboration

Roberta Manuela Moretti 1 collaboration

Marina Montagnani Marelli 1 collaboration

Giada Funghi 1 collaboration

Riccardo Chelli 1 collaboration

Vicenzo Conte 1 collaboration

Franklin Garcia-Godoy 1 collaboration

Umberto M Musazzi 1 collaboration

Silvia Franzè 1 collaboration

Paola Minghetti 1 collaboration

Giorgio Di Paco 1 collaboration

Giorgia Moschetti 1 collaboration

Daniela Maftei 1 collaboration

Roberta Lattanzi 1 collaboration

Valentina Onnis 1 collaboration

Alberto Panerai 1 collaboration

Hasret Subak 1 collaboration

Giulia Selvolini 1 collaboration

Dilsat Ozkan-Ariksoysal 1 collaboration

Giovanna Marrazza 1 collaboration

Lorenzo Casbarra 1 collaboration

Stefano Bellosta 1 collaboration

Giulia Magri 1 collaboration

Silvia Castiglioni 1 collaboration

Valerio Tolva 1 collaboration

Clara Rossi 1 collaboration

Francesco Puoci 1 collaboration

Francesco Cilurzo 1 collaboration

Zhaoxi Sun 1 collaboration