Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods

Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

(2018) Casper Steinmann et al.   Journal of Chemical Theory and Computation

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

(2017) Martin A. Olsson et al.   Journal of Chemical Theory and Computation

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

(2016) Ulf Ryde et al.   CHEMICAL REVIEWS

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level

(2016) Martin A. Olsson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands

(2016) Matthew R. Sullivan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)

(2016) Octav Caldararu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics

(2015) Jens Antony et al.   CHEMICAL COMMUNICATIONS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

(2015) Phillip S. Hudson et al.   Journal of Physical Chemistry Letters

Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods

(2015) Jan H. Jensen   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

ITC and NMR analysis of the encapsulation of fatty acids within a water-soluble cavitand and its dimeric capsule

(2015) Kaiya Wang et al.   SUPRAMOLECULAR CHEMISTRY

Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems

(2014) Milica Andrejić et al.   CHEMPHYSCHEM

A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

(2014) Paulius Mikulskis et al.   Journal of Chemical Information and Modeling

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Extension of the Universal Force Field to Metal–Organic Frameworks

(2014) Matthew A. Addicoat et al.   Journal of Chemical Theory and Computation

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

(2014) Paulius Mikulskis 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

Blind Prediction of Binding Affinities for Charged Supramolecular Host–Guest Systems: Achievements and Shortcomings of DFT-D3

(2014) Rebecca Sure et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An efficient and near linear scaling pair natural orbital based local coupled cluster method

(2013) Christoph Riplinger et al.   JOURNAL OF CHEMICAL PHYSICS

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

(2013) Joseph W. Kaus 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

Turbomole

(2013) Filipp Furche et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory

(2012) Stefan Grimme   CHEMISTRY-A EUROPEAN JOURNAL

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

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

Theoretical studies of HIV-1 reverse transcriptase inhibition

(2012) Katarzyna Świderek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Use of quantum mechanics/molecular mechanics-based FEP method for calculating relative binding affinities of FBPase inhibitors for type-2 diabetes

(2012) R. S. Rathore et al.   THEORETICAL CHEMISTRY ACCOUNTS

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Nonmonotonic Assembly of a Deep-Cavity Cavitand

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

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields

(2010) Martin Korth   Journal of Chemical Theory and Computation

Computing ensembles of transitions from stable states: Dynamic importance sampling

(2010) Juan R. Perilla et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

How to obtain statistically converged MM/GBSA results

(2009) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

(2009) Aleksandr V. Marenich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Host−Guest Complexes with Protein−Ligand-like Affinities: Computational Analysis and Design

(2009) Sarvin Moghaddam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-definition self-assemblies driven by the hydrophobic effect: synthesis and properties of a supramolecular nanocapsule

(2008) Simin Liu et al.   CHEMICAL COMMUNICATIONS

Theoretical and Practical Considerations in Virtual Screening: A Beaten Field?

(2008) Maria Kontoyianni et al.   CURRENT MEDICINAL CHEMISTRY

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Calorimetric Analysis of the 1:1 Complexes Formed between a Water-soluble Deep-cavity Cavitand, and Cyclic and Acyclic Carboxylic Acids

(2008) Hao Sun et al.   SUPRAMOLECULAR CHEMISTRY