SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach

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

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

(2017) Piero Procacci et al.   Journal of Chemical Theory and Computation

Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework

(2017) Edoardo Giovannelli et al.   Journal of Chemical Theory and Computation

Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation

(2017) Edoardo Giovannelli et al.   Journal of Chemical Theory and Computation

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

Overview of the SAMPL5 host–guest challenge: Are we doing better?

(2016) Jian Yin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2016) Piero Procacci   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands

(2016) Francesca Nerattini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular containers assembled through the hydrophobic effect

(2015) Jacobs H. Jordan et al.   CHEMICAL SOCIETY REVIEWS

Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

(2015) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions

(2015) Levi N. Naden et al.   Journal of Chemical Theory and Computation

Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations

(2015) Robert B. Sandberg et al.   Journal of Chemical Theory and Computation

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

Combining path-breaking with bidirectional nonequilibrium simulations to improve efficiency in free energy calculations

(2014) Edoardo Giovannelli et al.   JOURNAL OF CHEMICAL PHYSICS

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

(2014) Piero Procacci et al.   Journal of Chemical Theory and Computation

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Guest-mediated switching of the assembly state of a water-soluble deep-cavity cavitand

(2013) Haiying Gan et al.   CHEMICAL COMMUNICATIONS

Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations

(2013) Piero Procacci et al.   Journal of Chemical Theory and Computation

Binding of cyclic carboxylates to octa-acid deep-cavity cavitand

(2013) Corinne L. D. Gibb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations

(2009) Daniel K. Shenfeld et al.   PHYSICAL REVIEW E