Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

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

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

(2014) Gerhard König et al.   Journal of Chemical Theory and Computation

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

(2014) Gerhard König et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation

(2014) Christopher Cave-Ayland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein–Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase

(2014) Christopher J. Woods et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculating the Sensitivity and Robustness of Binding Free Energy Calculations to Force Field Parameters

(2013) Gabriel J. Rocklin et al.   Journal of Chemical Theory and Computation

Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies

(2013) Stephen J. Fox et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations

(2013) Frithjof Godschalk et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory

(2012) Stefan Grimme   CHEMISTRY-A EUROPEAN JOURNAL

Perspective: Alchemical free energy calculations for drug discovery

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

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

(2012) LiHong Hu et al.   Journal of Chemical Theory and Computation

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

(2012) Jiajing Zhang et al.   Journal of Chemical Theory and Computation

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

(2012) Richard Lonsdale et al.   Journal of Chemical Theory and Computation

Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents

(2012) William L. Jorgensen et al.   Journal of Chemical Theory and Computation

Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory

(2012) Jens Antony et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of SAMPL3 host–guest binding affinities: evaluating the accuracy of generalized force-fields

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

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling

(2012) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

(2012) Jimmy Heimdal 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

Can the protonation state of histidine residues be determined from molecular dynamics simulations?

(2012) Jon Uranga et al.   Computational and Theoretical Chemistry

Perspectives on halogen bonding and other σ-hole interactions: Lex parsimoniae (Occam’s Razor)

(2012) Peter Politzer et al.   Computational and Theoretical Chemistry

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

Protein–Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods

(2011) Jens Antony et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

(2011) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations

(2011) Frank R. Beierlein et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

(2011) Samuel Genheden et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Higher-order correlated calculations based on fragment molecular orbital scheme

(2011) Yuji Mochizuki et al.   THEORETICAL CHEMISTRY ACCOUNTS

QM/MM Approaches in Medicinal Chemistry Research

(2010) Lochana Menikarachchi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

Limits of Free Energy Computation for Protein−Ligand Interactions

(2010) Kenneth M. Merz   Journal of Chemical Theory and Computation

Ligand Affinities Estimated by Quantum Chemical Calculations

(2010) Pär Söderhjelm et al.   Journal of Chemical Theory and Computation

Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules

(2010) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect

(2010) Toshihiko Sawada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An MM/3D-RISM Approach for Ligand Binding Affinities

(2010) Samuel Genheden et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizable Water Molecules in Ligand−Macromolecule Recognition. Impact on the Relative Affinities of Competing Pyrrolopyrimidine Inhibitors for FAK Kinase

(2010) Benoit de Courcy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

(2010) Carl Diehl et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

QM/MM Methods for Biomolecular Systems

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

Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach

(2009) Marius Retegan et al.   Journal of Chemical Information and Modeling

MOLCAS 7: The Next Generation

(2009) Francesco Aquilante et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Calculation of Protein−Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects

(2009) Pär Söderhjelm et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations

(2009) Katherine E. Shaw et al.   Journal of Physical Chemistry Letters

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

(2008) Christopher J. Woods et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

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

How Accurate Can a Force Field Become? A Polarizable Multipole Model Combined with Fragment-wise Quantum-Mechanical Calculations

(2008) Pär Söderhjelm et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Interpretation of Protein/Ligand Crystal Structure using QM/MM Calculations: Case of HIV-1 Protease/Metallacarborane Complex

(2008) Jindřich Fanfrlík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A QM/MM study of fluoroaromatic interactions at the binding site of carbonic anhydrase II, using a DFT method corrected for dispersive interactions

(2008) Claudio A. Morgado et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Calculation of protein-ligand binding free energy by using a polarizable potential

(2008) D. Jiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA