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

Molecules (Basel, Switzerland), 2022-07, Vol.27 (14), p.4426

Procacci, Piero

2022

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

The Journal of chemical physics, 2019-10, Vol.151 (14), p.144115-144115

Procacci, Piero

2019

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Comment on “Statistical efficiency of methods for computing free energy of hydration” [J. Chem. Phys. 149, 144111 (2018)]

The Journal of chemical physics, 2019-03, Vol.150 (12), p.127101-127101

Procacci, Piero

2019

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

Journal of computer-aided molecular design, 2020-06, Vol.34 (6), p.635-639

Procacci, Piero

2020

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Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

The Journal of chemical physics, 2015-04, Vol.142 (15), p.154117-154117

Procacci, Piero

2015

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Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to

Journal of molecular graphics & modelling, 2017-01, Vol.71, p.233-241

Procacci, Piero

2017

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SAMPL9 blind predictions using nonequilibrium alchemical approaches

The Journal of chemical physics, 2022-04, Vol.156 (16), p.164104-164104

2022

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

The Journal of chemical physics, 2023-03, Vol.158 (12), p.124117-124117

2023

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SAMPL7 blind predictions using nonequilibrium alchemical approaches

Journal of computer-aided molecular design, 2021, Vol.35 (1), p.37-47

2021

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Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

Journal of chemical theory and computation, 2017-05, Vol.13 (5), p.1924-1933

2017

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

Journal of molecular graphics & modelling, 2022-01, Vol.110, p.108042-108042, Article 108042

2022

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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, 2021-06, Vol.35 (6), p.721-729

2021

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

Journal of computer-aided molecular design, 2021-10, Vol.35 (10), p.1055-1065

2021

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

Journal of computer-aided molecular design, 2020-04, Vol.34 (4), p.371-384

2020

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

Current opinion in structural biology, 2021-04, Vol.67, p.127-134

Procacci, Piero

2021

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Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling

Chemical physics letters, 2020-07, Vol.750, p.137489-137489, Article 137489

2020

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Mycotoxins aptasensing: From molecular docking to electrochemical detection of deoxynivalenol

Bioelectrochemistry (Amsterdam, Netherlands), 2021-04, Vol.138, p.107691-107691, Article 107691

2021

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Mounting evidence of FKBP12 implication in neurodegeneration

Neural regeneration research, 2020-12, Vol.15 (12), p.2195-2202

2020

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

Journal of chemical theory and computation, 2023-12, Vol.19 (23), p.8942-8954

Procacci, Piero

2023

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

Physical chemistry chemical physics : PCCP, 2019-07, Vol.21 (25), p.13826-13834

Procacci, Piero

2019

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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, 2017-06, Vol.57 (6), p.1240-1245

Procacci, Piero

2017

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

The Journal of chemical physics, 2019-10, Vol.151 (14), p.144113-144113

Procacci, Piero

2019

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

Journal of chemical theory and computation, 2022-06, Vol.18 (6), p.4014-4026

Procacci, Piero

2022

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Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations

Journal of chemical information and modeling, 2016-06, Vol.56 (6), p.1117-1121

Procacci, Piero

2016

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I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework

Physical chemistry chemical physics : PCCP, 2016-06, Vol.18 (22), p.14991-15004

Procacci, Piero

2016

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

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

Comment on “Statistical efficiency of methods for computing free energy of hydration” [J. Chem. Phys. 149, 144111 (2018)]

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

Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to

SAMPL9 blind predictions using nonequilibrium alchemical approaches

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

SAMPL7 blind predictions using nonequilibrium alchemical approaches

Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories

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

Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

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

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

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

Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling

Mycotoxins aptasensing: From molecular docking to electrochemical detection of deoxynivalenol

Mounting evidence of FKBP12 implication in neurodegeneration

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

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

PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules

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

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

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework

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