NE‐RDFE : A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes

Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method

(2022) Solmaz Azimi et al.   Journal of Chemical Information and Modeling

SAMPL9 blind predictions using nonequilibrium alchemical approaches

(2022) Piero Procacci et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2022) Piero Procacci   Journal of Chemical Theory and Computation

Exploring the Effect of Enhanced Sampling on Protein Stability Prediction

(2022) Daniel Markthaler et al.   Journal of Chemical Theory and Computation

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

(2022) Piero Procacci   MOLECULES

Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations

(2021) Hannah M. Baumann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

(2021) Vytautas Gapsys et al.   Communications Chemistry

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

(2021) Junjie Zou et al.   Journal of Chemical Theory and Computation

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

(2021) Marina Macchiagodena et al.   Journal of Chemical Information and Modeling

Thermodynamics of pillararene·guest complexation: blinded dataset for the SAMPL9 challenge

(2021) Chun-Lin Deng et al.   NEW JOURNAL OF CHEMISTRY

Rigorous Free Energy Simulations in Virtual Screening

(2020) Zoe Cournia et al.   Journal of Chemical Information and Modeling

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

(2020) Piero Procacci   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using AMBER18 for Relative Free Energy Calculations

(2019) Lin Frank Song et al.   Journal of Chemical Information and Modeling

Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations

(2019) Rajat K. Pal et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2019) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

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

(2017) Piero Procacci   Journal of Chemical Information and Modeling

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

(2017) Piero Procacci   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

(2017) Leela S. Dodda et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Piero Procacci   Journal of Chemical Information and Modeling

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

(2016) Lingle Wang et al.   Journal of Chemical Theory and Computation

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

(2015) Shuai Liu et al.   Journal of Chemical Information and Modeling

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

(2012) Vytautas Gapsys et al.   Journal of Chemical Theory and Computation

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

(2012) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Scaffold-Hopping Strategy: Synthesis and Biological Evaluation of 5,6-Fused Bicyclic Heteroaromatics To Identify Orally Bioavailable Anticancer Agents

(2011) Yen-Shih Tung et al.   JOURNAL OF MEDICINAL CHEMISTRY

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

(2009) Simone Marsili et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY