Articoli con mandati relativi all'accesso pubblico - Piero ProcacciUlteriori informazioni
Non disponibili pubblicamente: 6
Fast switching alchemical transformations in molecular dynamics simulations
P Procacci, C Cardelli
Journal of Chemical Theory and Computation 10 (7), 2813-2823, 2014
Mandati: Governo Italiano
Hybrid MPI/OpenMP implementation of the ORAC molecular dynamics program for generalized ensemble and fast switching alchemical simulations
P Procacci
Journal of chemical information and modeling 56 (6), 1117-1121, 2016
Mandati: Governo Italiano
Upgrading and validation of the AMBER force field for histidine and cysteine zinc (II)-binding residues in sites with four protein ligands
M Macchiagodena, M Pagliai, C Andreini, A Rosato, P Procacci
Journal of Chemical Information and Modeling 59 (9), 3803-3816, 2019
Mandati: Governo Italiano
Energy-driven undocking (edu-hrem) in solute tempering replica exchange simulations
P Procacci, M Bizzarri, S Marsili
Journal of Chemical Theory and Computation 10 (1), 439-450, 2014
Mandati: Governo Italiano
Evidence of a low–high density turning point in liquid water at ordinary temperature under pressure: a molecular dynamics study
M Pagliai, M Macchiagodena, P Procacci, G Cardini
The Journal of Physical Chemistry Letters 10 (20), 6414-6418, 2019
Mandati: Governo Italiano
Nonequilibrium Alchemical Simulations for the Development of Drugs Against Covid-19
M Macchiagodena, M Karrenbrock, M Pagliai, G Guarnieri, F Iannone, ...
In Silico Modeling of Drugs Against Coronaviruses: Computational Tools and …, 2021
Mandati: Governo Italiano
Disponibili pubblicamente: 38
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
D Vassetti, M Pagliai, P Procacci
Journal of chemical theory and computation 15 (3), 1983-1995, 2019
Mandati: Governo Italiano
Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling
M Macchiagodena, M Pagliai, P Procacci
Chemical Physics Letters 750, 137489, 2020
Mandati: Governo Italiano
PrimaDORAC: a free web interface for the assignment of partial charges, chemical topology, and bonded parameters in organic or drug molecules
P Procacci
Journal of chemical information and modeling 57 (6), 1240-1245, 2017
Mandati: Governo Italiano
Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease
M Macchiagodena, M Pagliai, P Procacci
Journal of Molecular Graphics and Modelling 110, 108042, 2022
Mandati: Governo Italiano
II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands
F Nerattini, R Chelli, P Procacci
Physical Chemistry Chemical Physics 18 (22), 15005-15018, 2016
Mandati: Governo Italiano
Thia-bridged triarylamine heterohelicene radical cations as redox-driven molecular switches
S Menichetti, S Cecchi, P Procacci, M Innocenti, L Becucci, L Franco, ...
Chemical Communications 51 (57), 11452-11454, 2015
Mandati: Governo Italiano
I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework
P Procacci
Physical Chemistry Chemical Physics 18 (22), 14991-15004, 2016
Mandati: Governo Italiano
SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach
P Procacci, M Guarrasi, G Guarnieri
Journal of computer-aided molecular design 32, 965-982, 2018
Mandati: Governo Italiano
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
M Macchiagodena, M Pagliai, M Karrenbrock, G Guarnieri, F Iannone, ...
Journal of Chemical Theory and Computation 16 (11), 7160-7172, 2020
Mandati: Governo Italiano
Upgraded AMBER force field for zinc-binding residues and ligands for predicting structural properties and binding affinities in zinc-proteins
M Macchiagodena, M Pagliai, C Andreini, A Rosato, P Procacci
ACS omega 5 (25), 15301-15310, 2020
Mandati: European Commission, Governo Italiano
Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations
P Procacci, M Macchiagodena, M Pagliai, G Guarnieri, F Iannone
Chemical Communications 56 (62), 8854-8856, 2020
Mandati: Governo Italiano
Solvation free energies via alchemical simulations: let's get honest about sampling, once more
P Procacci
Physical Chemistry Chemical Physics 21 (25), 13826-13834, 2019
Mandati: Governo Italiano
SAMPL7 blind predictions using nonequilibrium alchemical approaches
P Procacci, G Guarnieri
Journal of Computer-Aided Molecular Design 35, 37-47, 2021
Mandati: Governo Italiano
Virtual double-system single-box for absolute dissociation free energy calculations in GROMACS
M Macchiagodena, M Karrenbrock, M Pagliai, P Procacci
Journal of Chemical Information and Modeling 61 (11), 5320-5326, 2021
Mandati: Governo Italiano
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