Piero Procacci
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View article: Achieving Chemical Accuracy in Cyclodextrin Host–Guest Binding via Integrative Atomistic Modelling
Achieving Chemical Accuracy in Cyclodextrin Host–Guest Binding via Integrative Atomistic Modelling Open
Cyclodextrins are amphiphilic macromolecular containers that are particularly valuable in applications ranging from biomedicine to environmental science. Despite years of development of computational techniques for cyclodextrin host‐guest …
View article: Fluorinated Alcohol Biosolvents and α-helix Peptide Secondary Structure: a Molecular Dynamics Study on Solvent Concentration Effect
Fluorinated Alcohol Biosolvents and α-helix Peptide Secondary Structure: a Molecular Dynamics Study on Solvent Concentration Effect Open
An upgraded GAFF2 force field has been used to simulate two fluorinated alcohols, TFE and HFIP, in aqueous solutions at several concentrations. The same force field has also been employed to simulate a 26-residue amphiphilic peptide in sev…
View article: Combining QCM and SERS on a Nanophotonic Chip: A Dual-Functional Sensor for Biomolecular Interaction Analysis and Protein Fingerprinting
Combining QCM and SERS on a Nanophotonic Chip: A Dual-Functional Sensor for Biomolecular Interaction Analysis and Protein Fingerprinting Open
We present a dual biosensing strategy integrating Quartz Crystal Microbalance (QCM) and Surface-Enhanced Raman Spectroscopy (SERS) for the quantitative and molecular-specific detection of FKBP12. Silver nanodendritic arrays were electrodep…
View article: Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6–31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches
Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6–31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches Open
We assess the performance of the nonequilibrium alchemical fast-growth method in calculating water and 1-octanol solvation free energies, comparing the recently proposed ABCG2 model with other empirical and quantum mechanics (QM)-based app…
View article: Ultrasensitive Detection of FKBP12 Using a Synthetic Receptor‐Functionalized QCM Nanoplatform
Ultrasensitive Detection of FKBP12 Using a Synthetic Receptor‐Functionalized QCM Nanoplatform Open
FKBP12, a peptidyl‐prolyl isomerase implicated in cancer, neurodegenerative diseases, and post‐transplant anti‐rejection mechanisms, represents a critical biomarker for early diagnosis and monitoring. Here, a novel diagnostic nanoplatform …
View article: Development of a New AMBER Force Field for Cysteine and Histidine Cadmium‐Binding Proteins and Its Validation Through QM/MM MD Simulations
Development of a New AMBER Force Field for Cysteine and Histidine Cadmium‐Binding Proteins and Its Validation Through QM/MM MD Simulations Open
We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of cadmium(II)‐binding proteins. The proposed force field takes into account the polarization effect produced by the central ion…
View article: PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files
PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files Open
We present PDBrestore, a free web interface for repairing protein PDB chains extracted from either a local PDB file or a PDB file downloaded from the Protein Data Bank. PDBrestore performs several key tasks: It adds hydrogen atoms, complet…
View article: Antiproliferative Role of Natural and Semi-Synthetic Tocopherols on Colorectal Cancer Cells Overexpressing the Estrogen Receptor β
Antiproliferative Role of Natural and Semi-Synthetic Tocopherols on Colorectal Cancer Cells Overexpressing the Estrogen Receptor β Open
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 of this receptor is inversely related to …
View article: Front Cover: Identification of Potential Inhibitors of the SARS‐CoV‐2 NSP13 Helicase via Structure‐Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations (ChemMedChem 10/2024)
Front Cover: Identification of Potential Inhibitors of the SARS‐CoV‐2 NSP13 Helicase via Structure‐Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations (ChemMedChem 10/2024) Open
The Front Cover shows the NSP13 helicase, catalyzing the unwinding of viral RNA in the virus replication, represents a promising target for designing broad-spectrum antiviral drugs. Inhibition of this protein could be achieved by designing…
View article: Identification of Potential Inhibitors of the SARS‐CoV‐2 NSP13 Helicase via Structure‐Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations
Identification of Potential Inhibitors of the SARS‐CoV‐2 NSP13 Helicase via Structure‐Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations Open
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 by …
View article: Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations
Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations Open
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 (crystallographic) pose.…
View article: Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host–guest systems
Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host–guest systems Open
Using an alchemical simulation technique, we assess the impact of force fields, ionic strength and guest charge neutralization on the computed dissociation free energies in heavily charged macrocyclic hosts recently used in SAMPL challenge…
View article: Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions
Dealing with Induced Fit, Conformational Selection, and Secondary Poses in Molecular Dynamics Simulations for Reliable Free Energy Predictions Open
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 two macrocyclic hosts for…
View article: Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions
Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions Open
In this study we have tested the performance of standard molecular dynamics simulations (MD), replicates of shorter standard MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for the sampling of two macrocyclic hosts for …
View article: Addressing sub-optimal poses in non-equilibrium alchemical calculations
Addressing sub-optimal poses in non-equilibrium alchemical calculations Open
Alchemical transformations can be used to quantitatively estimate absolute binding free energies at reasonable computational cost. However, most of the approaches currently in use require knowledge of the correct (crystallographic) bond po…
View article: Supporting Material: Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations
Supporting Material: Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations Open
Supporting Material: Addressing Suboptimal Poses in Nonequilibrium Alchemical CalculationsAddressing Suboptimal Poses in Nonequilibrium Alchemical CalculationsMaurice Karrenbrock, Valerio Rizzi, Piero Procacci, and Francesco Luigi Gervasio…
View article: Supporting Material: Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations
Supporting Material: Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations Open
Supporting Material: Addressing Suboptimal Poses in Nonequilibrium Alchemical CalculationsAddressing Suboptimal Poses in Nonequilibrium Alchemical CalculationsMaurice Karrenbrock, Valerio Rizzi, Piero Procacci, and Francesco Luigi Gervasio…
View article: Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions
Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions Open
In this study we have tested the performance of standard molecular dynamics simulations (MD), replicates of shorter standard MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for the sampling of two macrocyclic hosts for …
View article: Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions
Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions Open
Essential data and s/w for the paper "Dealing with induced fit, conformational selection and secondary poses in molecular dynamics simulations for reliable free energy predictions" inputs directory: Contains the ORAC input files for all s…
View article: SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches
SAMPL9 blind predictions for toluene/water partition coefficients using nonequilibrium alchemical approaches Open
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, we used an efficient MD-based nonequil…
View article: A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints
A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints Open
In this paper we further develop a combined Hamiltonian replica exchange / non-equilibrium alchemical method for absolute binding free energies and test its performance on 11 ligands of the BRD4 bromodomain protein. We compare the results …
View article: Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints" Open
Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints". The directory is fully documented with README files. Differences of V2.0 with V1.0: …
View article: Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints" Open
Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints". The directory is fully documented with README files.
View article: Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints" Open
Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints". The directory is fully documented with README files. Differences of V2.0 with V1.0: …
View article: <scp>NE‐RDFE</scp>: A protocol and toolkit for computing relative dissociation free energies with <scp>GROMACS</scp> between dissimilar molecules using bidirectional nonequilibrium dual topology schemes
<span>NE‐RDFE</span>: A protocol and toolkit for computing relative dissociation free energies with <span>GROMACS</span> between dissimilar molecules using bidirectional nonequilibrium dual topology schemes Open
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 approach. The propose…
View article: Data for LogP toluene/water SAMPL9 challenge
Data for LogP toluene/water SAMPL9 challenge Open
Data for reproducing nonequilibrium fast growth (NE-FG) blind predictions of the toluene/water partition coefficients with the s/w ORAC6.1 (www1.chim.unifi.it/orac) This archive contains the following directories: lib-631Gd -> GAFF2 ORAC …
View article: Data for LogP toluene/water SAMPL9 challenge
Data for LogP toluene/water SAMPL9 challenge Open
Data for reproducing nonequilibrium fast growth (NE-FG) blind predictions of the toluene/water partition coefficients with the s/w ORAC6.1 (www1.chim.unifi.it/orac) This archive contains the following directories: lib-631Gd -> GAFF2 ORAC …