Piero Procacci
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Explore the profile of Piero Procacci including associated specialties, affiliations and a list of published articles.
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83
Citations
690
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Recent Articles
1.
Falsetti I, Palmini G, Zonefrati R, Vasa K, Donati S, Aurilia C, et al.
Int J Mol Sci
. 2025 Mar;
26(5).
PMID: 40076925
Estrogen receptor β (ERβ) is the most highly expressed subtype in the colon epithelium and mediates the protective effect of estrogen against the development of colon cancer. Indeed, the expression...
2.
Sun Z, Procacci P
Phys Chem Chem Phys
. 2024 Jul;
26(29):19887-19899.
PMID: 38990073
As a contribution to the understanding and rationalization of methodological and modeling effects in recent host-guest SAMPL challenges, using an alchemical molecular dynamics technique we have examined the impact of...
3.
Di Paco G, Macchiagodena M, Procacci P
ChemMedChem
. 2024 Mar;
19(10):e202400095.
PMID: 38456332
We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing...
4.
Karrenbrock M, Rizzi V, Procacci P, Gervasio F
J Phys Chem B
. 2024 Feb;
128(7):1595-1605.
PMID: 38323915
Alchemical transformations can be used to quantitatively estimate absolute binding free energies at a reasonable computational cost. However, most of the approaches currently in use require knowledge of the correct...
5.
Procacci P
J Chem Theory Comput
. 2023 Dec;
19(23):8942-8954.
PMID: 38037326
In this study, we have tested the performance of standard molecular dynamics (MD) simulations, replicates of shorter standard MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for the sampling of...
6.
Procacci P, Guarnieri G
J Chem Phys
. 2023 Apr;
158(12):124117.
PMID: 37003748
We present our blind prediction of the toluene-water partition coefficients in the context of the SAMPL9 challenge. For the calculation of the solvation free energies in water, toluene, and 1-octanol,...
7.
Macchiagodena M, Pagliai M, Procacci P
J Comput Chem
. 2023 Jan;
44(12):1221-1230.
PMID: 36704972
We describe a step-by-step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical...
8.
Macchiagodena M, Bassu G, Vettori I, Fratini E, Procacci P, Pagliai M
J Phys Chem A
. 2022 Nov;
126(47):8826-8833.
PMID: 36394997
Structural properties of 2-butanol aqueous solutions at different concentrations have been studied using small- and wide-angle X-ray scattering and molecular dynamics simulations. The experimental structure factors have been accurately reproduced...
9.
Procacci P
Molecules
. 2022 Jul;
27(14).
PMID: 35889299
In the context of computational drug design, we examine the effectiveness of the enhanced sampling techniques in state-of-the-art free energy calculations based on alchemical molecular dynamics simulations. In a paradigmatic...
10.
Procacci P
J Chem Theory Comput
. 2022 Jun;
18(6):4014-4026.
PMID: 35642423
In the context of advanced hit-to-lead drug design based on atomistic molecular dynamics simulations, we propose a dual topology alchemical approach for calculating the relative binding free energy (RBFE) between...