Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

Cucurbituril-Based Molecular Recognition

(2015) Steven J. Barrow et al.   CHEMICAL REVIEWS

Evaluation of GalaxyDock Based on the Community Structure–Activity Resource 2013 and 2014 Benchmark Studies

(2015) Woong-Hee Shin et al.   Journal of Chemical Information and Modeling

Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method

(2015) Juyong Lee et al.   Journal of Chemical Theory and Computation

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge

(2015) Emilio Gallicchio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Acyclic cucurbit[n]uril-type molecular containers: influence of glycoluril oligomer length on their function as solubilizing agents

(2015) Laura Gilberg et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Computational scheme for pH-dependent binding free energy calculation with explicit solvent

(2015) Juyong Lee et al.   PROTEIN SCIENCE

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

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

(2014) Juyong Lee et al.   Journal of Chemical Theory and Computation

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field

(2014) Francesco Manzoni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge

(2014) Libo Li et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

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

Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge

(2014) Lars Sandberg   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Extended solvent-contact model approach to SAMPL4 blind prediction challenge for hydration free energies

(2014) Hwangseo Park   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory

(2014) Jia Fu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

(2014) Jacob I. Monroe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of HIV integrase binding from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

(2014) Emilio Gallicchio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field

(2014) Oliver Beckstein et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics

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

Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK

(2014) Benjamin A. Ellingson et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blind prediction of solvation free energies from the SAMPL4 challenge

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge

(2014) Alexander L. Perryman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge

(2014) Hervé Hogues 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

The SAMPL4 host–guest blind prediction challenge: an overview

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

Acyclic Cucurbit[n]uril-type Molecular Containers: Influence of Aromatic Walls on their Function as Solubilizing Excipients for Insoluble Drugs

(2014) Ben Zhang et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

The Movable Type Method Applied to Protein–Ligand Binding

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

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides

(2013) Satoru G. Itoh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies

(2013) Anita de Ruiter et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

(2013) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

(2012) Gerhard König et al.   Journal of Chemical Theory and Computation

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

(2012) Wenbo Yu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set

(2012) Jens Reinisch et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A fragment-based approach to the SAMPL3 Challenge

(2012) John L. Kulp et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

(2012) Emilio Gallicchio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge

(2012) Ashutosh Kumar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The SAMPL3 blind prediction challenge: transfer energy overview

(2012) Matthew T. Geballe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Modularity optimization by conformational space annealing

(2012) Juyong Lee et al.   PHYSICAL REVIEW E

Software and resources for computational medicinal chemistry

(2011) Chenzhong Liao et al.   Future Medicinal Chemistry

LigDockCSA: Protein-ligand docking using conformational space annealing

(2011) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Avoiding the van der Waals endpoint problem using serial atomic insertion

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

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations

(2011) Gerhard König et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

(2011) Juyong Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Cucurbituril chemistry: a tale of supramolecular success

(2011) Eric Masson et al.   RSC Advances

Benzobis(imidazolium)-Cucurbit[8]uril Complexes for Binding and Sensing Aromatic Compounds in Aqueous Solution

(2010) Frank Biedermann et al.   CHEMISTRY-A EUROPEAN JOURNAL

Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules

(2010) Satoru G. Itoh et al.   JOURNAL OF CHEMICAL PHYSICS

Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration

(2010) Stefan Bruckner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Acyclic Cucurbit[n]uril Congeners Are High Affinity Hosts

(2010) Da Ma et al.   JOURNAL OF ORGANIC CHEMISTRY

Unorthodox uses of Bennett's acceptance ratio method

(2009) Gerhard König et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY