Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host–Guest Systems

NE‐RDFE : A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes

(2023) Marina Macchiagodena et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Modelling of Ionic Liquids: Situations When Charge Scaling Seems Insufficient

(2023) Zhaoxi Sun et al.   MOLECULES

Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score

(2023) Rikuri Morita et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular modelling of ionic liquids: Perfluorinated anionic species with enlarged halogen substitutions

(2023) Zhaoxi Sun et al.   JOURNAL OF MOLECULAR LIQUIDS

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

(2023) Xiao Liu et al.   MOLECULES

A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions

(2023) Zhaoxi Sun et al.   MOLECULES

Host Dynamics under General-Purpose Force Fields

(2023) Xiaohui Wang et al.   MOLECULES

PSMA-Targeted Supramolecular Nanoparticles Prepared From Cucurbit[8]uril-Based Ternary Host–Guest Recognition for Prostate Cancer Therapy

(2022) Xueyan Zhang et al.   Frontiers in Chemistry

SAMPL9 blind predictions using nonequilibrium alchemical approaches

(2022) Piero Procacci et al.   JOURNAL OF CHEMICAL PHYSICS

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

Molecular modelling of ionic liquids: Physical properties of species with extremely long aliphatic chains from a near-optimal regime

(2022) Zhaoxi Sun et al.   JOURNAL OF MOLECULAR LIQUIDS

SAMPL7 blind predictions using nonequilibrium alchemical approaches

(2021) Piero Procacci et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Photoresponsive Binding Dynamics in High‐Affinity Cucurbit[8]uril‐Dithienylethene Host‐Guest Complexes

(2021) Nuno Basílio et al.   CHEMISTRY-A EUROPEAN JOURNAL

Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis

(2021) Jianzhong Chen et al.   Journal of Chemical Information and Modeling

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

DFT-D4 Insight into the Inclusion of Amphetamine and Methamphetamine in Cucurbit[7]uril: Energetic, Structural and Biosensing Properties

(2021) Abdelkarim Litim et al.   MOLECULES

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

DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method

(2020) Yanyi Chu et al.   BRIEFINGS IN BIOINFORMATICS

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

Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics

(2020) Piero Procacci   CURRENT OPINION IN STRUCTURAL BIOLOGY

Host–guest interactions in nor-seco-cucurbit[10]uril: novel guest-dependent molecular recognition and stereoisomerism

(2019) Xiaodong Zhang et al.   Beilstein Journal of Organic Chemistry

Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees

(2019) Li Li et al.   Scientific Reports

Structural Effects on Guest Binding in Cucurbit[8]uril-Perylenemonoimide Host-Guest Complexes

(2018) Gyan H. Aryal et al.   ChemistrySelect

SAMPL6 host–guest challenge: binding free energies via a multistep approach

(2018) Yiğitcan Eken et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Accurate and Efficient Calculation of Protein–Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants

(2018) Xiao Liu et al.   Journal of Chemical Information and Modeling

Cucurbit[8]uril•guest complexes: blinded dataset for the SAMPL6 challenge

(2018) Steven Murkli et al.   SUPRAMOLECULAR CHEMISTRY

Terpenes Show Nanomolar Affinity and Selective Binding with Cucurbit[8]uril

(2017) Miguel A. Romero et al.   ISRAEL JOURNAL OF CHEMISTRY

Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation

(2017) Edoardo Giovannelli et al.   Journal of Chemical Theory and Computation

HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host–Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions

(2017) Khaleel I. Assaf et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water models for biomolecular simulations

(2017) Alexey V. Onufriev et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Inclusion compound based on Bis(ethylenediamine)copper(II) complex and cucurbit[8]uril: Quantum chemical prediction for structure and formation thermodynamic parameters

(2015) T. N. Grishaeva et al.   RUSSIAN JOURNAL OF INORGANIC CHEMISTRY

Density functional investigations on 2-naphthalenecarbonitrile dimerization within cucurbit[8]uril cavitand

(2014) Swarada R. Peerannawar et al.   JOURNAL OF MOLECULAR MODELING

Calculation of Host–Guest Binding Affinities Using a Quantum-Mechanical Energy Model

(2012) Hari S. Muddana et al.   Journal of Chemical Theory and Computation

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

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

Size Selective Supramolecular Cages from Aryl-Bisimidazolium Derivatives and Cucurbit[8]uril

(2011) Dezhi Jiao et al.   ORGANIC LETTERS

Cucurbituril chemistry: a tale of supramolecular success

(2011) Eric Masson et al.   RSC Advances

Correlating Solution Binding and ESI-MS Stabilities by Incorporating Solvation Effects in a Confined Cucurbit[8]uril System

(2010) Urs Rauwald et al.   JOURNAL OF PHYSICAL CHEMISTRY B

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Effects of the number and placement of positive charges on viologen–cucurbit[n]uril interactions

(2008) Gretchen A. Vincil et al.   SUPRAMOLECULAR CHEMISTRY