Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

Probing the Binding Affinity by Jarzynski’s Nonequilibrium Binding Free Energy and Rupture Time

(2018) Duc Toan Truong et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Gibbs Sampler-Based λ-Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation

(2017) Xinqiang Ding et al.   Journal of Chemical Theory and Computation

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

(2016) Stefano Bosisio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Absolute binding free energies for octa-acids and guests in SAMPL5

(2016) Florentina Tofoleanu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

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

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

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

Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics

(2016) Soumendranath Bhakat et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

(2016) Nupur Bansal et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations

(2015) Kira A. Armacost et al.   Journal of Chemical Theory and Computation

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

(2015) Niel M. Henriksen 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

A Simple Assay for Quality Binders to Cucurbiturils

(2014) Julián Vázquez  et al.   CHEMISTRY-A EUROPEAN JOURNAL

Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”

(2014) Melek N. Ucisik et al.   Journal of Chemical Theory and Computation

Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics

(2014) Ya-Wen Hsiao et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL4 host–guest blind prediction challenge: an overview

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

Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2

(2014) Germano Heinzelmann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering

(2012) Lianqing Zheng et al.   Journal of Chemical Theory and Computation

Force and Stress along Simulated Dissociation Pathways of Cucurbituril–Guest Systems

(2012) Camilo Velez-Vega et al.   Journal of Chemical Theory and Computation

Computation of the binding affinities of catechol-O-methyltransferase inhibitors: Multisubstate relative free energy calculations

(2012) P. Nuno Palma et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Blind prediction of host–guest binding affinities: a new SAMPL3 challenge

(2012) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Cucurbit[8]uril Mediated Donor–Acceptor Ternary Complexes: A Model System for Studying Charge-Transfer Interactions

(2012) Frank Biedermann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Alchemical free energy methods for drug discovery: progress and challenges

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

Model for the fast estimation of basis set superposition error in biomolecular systems

(2011) John C. Faver et al.   JOURNAL OF CHEMICAL PHYSICS

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein−Ligand Complexes

(2011) John C. Faver et al.   Journal of Chemical Theory and Computation

Nonmonotonic Assembly of a Deep-Cavity Cavitand

(2011) Haiying Gan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Test MM-PB/SA on True Conformational Ensembles of Protein−Ligand Complexes

(2010) Yan Li et al.   Journal of Chemical Information and Modeling

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

(2010) James Luccarelli et al.   Journal of Chemical Theory and Computation

Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations

(2009) F. Marty Ytreberg   JOURNAL OF CHEMICAL PHYSICS

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

(2009) Slimane Doudou et al.   Journal of Chemical Theory and Computation

λ-Dynamics free energy simulation methods

(2009) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

(2008) Michel A. Cuendet et al.   BIOPHYSICAL JOURNAL

Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex

(2008) Harish Vashisth et al.   BIOPHYSICAL JOURNAL

The role of ABC transporters in drug absorption, distribution, metabolism, excretion and toxicity (ADME–Tox)

(2008) Gergely Szakács et al.   DRUG DISCOVERY TODAY

Bornyl (3,4,5-trihydroxy)-cinnamate - An optimized human neutrophil elastase inhibitor designed by free energy calculations

(2007) Thomas Steinbrecher et al.   BIOORGANIC & MEDICINAL CHEMISTRY