Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein–Ligand Sampling

(2022) Wenlang Liu et al.   Journal of Chemical Information and Modeling

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure

(2022) Xiao Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Primary vs secondary: Directionalized guest coordination in β-cyclodextrin derivatives

(2022) Zhaoxi Sun et al.   CARBOHYDRATE POLYMERS

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

(2022) Xiao Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations

(2021) Zhe Huai et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

(2021) Jerome Eberhardt et al.   Journal of Chemical Information and Modeling

Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

(2021) Lorenzo Casbarra et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A General Picture of Cucurbit[8]uril Host–Guest Binding

(2021) Zhaoxi Sun et al.   Journal of Chemical Information and Modeling

SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations

(2020) Zhaoxi Sun et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations

(2020) Zhaoxi Sun   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SAMPL7 TrimerTrip host–guest binding affinities from extensive alchemical and end-point free energy calculations

(2020) Zhe Huai et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

(2020) Yuriy Khalak et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis

(2016) Changhao Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan et al.   Journal of Chemical Theory and Computation

Enhanced stability of a naringenin/2,6-dimethyl β-cyclodextrin inclusion complex: Molecular dynamics and free energy calculations based on MM- and QM-PBSA/GBSA

(2014) Waratchada Sangpheak et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

(2012) Samuel Genheden et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B