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

SAMPL7 blind predictions using nonequilibrium alchemical approaches

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

Ion Dynamics and Selectivity of Nav channels from Molecular Dynamics Simulation

(2021) Zhaoxi Sun et al.   CHEMICAL PHYSICS

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

An electrostatic energy-based charge model for molecular dynamics simulation

(2021) Xianwei Wang et al.   JOURNAL OF CHEMICAL PHYSICS

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

Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy

(2021) Martina Bertazzo et al.   Journal of Chemical Theory and Computation

SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules

(2021) Basak Koca Fındık et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

(2021) Hafiz Saqib Ali et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

BAR‐Based Multi‐Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

(2021) Zhaoxi Sun et al.   Advanced Theory and Simulations

Conformational Fluctuations in GTP-Bound K-Ras: A Metadynamics Perspective with Harmonic Linear Discriminant Analysis

(2021) Xiaohui Wang   Journal of Chemical Information and Modeling

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

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

Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE

(2021) Jakub Jurasz et al.   PLoS Computational Biology

Molecular Insight into the Interaction between Camptothecin and Acyclic Cucurbit[4]urils as Efficient Nanocontainers in Comparison with Cucurbit[7]uril: Molecular Docking and Molecular Dynamics Simulation

(2020) Nasim Ahmadian 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

Functional Supramolecular Polymeric Networks: The Marriage of Covalent Polymers and Macrocycle-Based Host–Guest Interactions

(2020) Danyu Xia et al.   CHEMICAL REVIEWS

Compulsive methamphetamine taking induces autophagic and apoptotic markers in the rat dorsal striatum

(2020) Rajeev Subu et al.   ARCHIVES OF TOXICOLOGY

Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach

(2020) Benjamin R. Jagger et al.   Journal of Chemical Theory and Computation

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

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

A fast and high-quality charge model for the next generation general AMBER force field

(2020) Xibing He et al.   JOURNAL OF CHEMICAL PHYSICS

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

Importance of base-pair opening for mismatch recognition

(2020) Tomáš Bouchal et al.   NUCLEIC ACIDS RESEARCH

Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields

(2020) Zhe Huai et al.   Journal of Chemical Information and Modeling

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

(2020) Piero Procacci   CURRENT OPINION IN STRUCTURAL BIOLOGY

Thermodynamics of Helix formation in small peptides of varying length in vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

(2019) Zhaoxi Sun et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

BAR‐based optimum adaptive steered MD for configurational sampling

(2019) Xiaohui Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

(2019) Jianzhong Chen et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation

(2019) Zhaoxi Sun et al.   CHEMICAL PHYSICS LETTERS

Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification

(2019) Xiaohui Wang et al.   Journal of Chemical Information and Modeling

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

Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics

(2019) Riccardo Capelli et al.   Journal of Physical Chemistry Letters

Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange

(2019) Z. Faidon Brotzakis et al.   JOURNAL OF CHEMICAL PHYSICS

Layered nested Markov chain Monte Carlo

(2018) Nicholas E. Jackson et al.   JOURNAL OF CHEMICAL PHYSICS

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification

(2018) Xiaohui Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Ketamine blocks bursting in the lateral habenula to rapidly relieve depression

(2018) Yan Yang et al.   NATURE

Reversible Encapsulations and Stimuli-Responsive Biological Delivery from Dynamically Assembled Cucurbit[7]uril Host and Nanoparticle Guest Scaffold

(2018) Santu Sinha et al.   Journal of Materials Chemistry B

From Levinthal`s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

(2018) Juan Zeng et al.   CURRENT MEDICINAL CHEMISTRY

Absolute binding free energies for the SAMPL6 cucurbit[8]uril host–guest challenge via the AMOEBA polarizable force field

(2018) Marie L. Laury et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Extensive Assessment of Various Computational Methods for Aspartate’s pKa Shift

(2017) Zhaoxi Sun et al.   Journal of Chemical Information and Modeling

Confinement induced thermodynamic and kinetic facilitation of some Diels-Alder reactions inside a CB[7] cavitand

(2017) Debdutta Chakraborty et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

(2017) Zhao X. Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multipole models of sulphur for accurate anisotropic electrostatic interactions within force fields

(2017) D. A. Shulga et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Heparan sulfate: Resilience factor and therapeutic target for cocaine abuse

(2017) Jihuan Chen et al.   Scientific Reports

Ketamine-Induced Apoptosis in Normal Human Urothelial Cells

(2016) Simon C. Baker et al.   AMERICAN JOURNAL OF PATHOLOGY

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

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

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

(2016) Noor Asidah Mohamed et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions

(2016) Jerônimo Lameira et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Brain Reward Circuits in Morphine Addiction

(2016) Juhwan Kim et al.   MOLECULES AND CELLS

II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands

(2016) Francesca Nerattini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ketamine in refractory convulsive status epilepticus in children avoids endotracheal intubation

(2015) Lucrezia Ilvento et al.   EPILEPSY & BEHAVIOR

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

(2015) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms

(2015) Yoshiharu Mori et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Folding Simulations of an α-Helical Hairpin Motif αtα with Residue-Specific Force Fields

(2015) Juan Zeng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ketamine and Midazolam Anesthesia in Pacific Martens (Martes caurina)

(2015) Jack A. Mortenson et al.   JOURNAL OF WILDLIFE DISEASES

Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex

(2015) D B McClatchy et al.   MOLECULAR PSYCHIATRY

Ketamine-An Update on Its Clinical Uses and Abuses

(2014) Jian Xu et al.   CNS Neuroscience & Therapeutics

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

(2014) Samuel Genheden 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

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

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

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Cocaine Cardiotoxicity

(2013) Katharine Phillips et al.   American Journal of Cardiovascular Drugs

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Faster absorption and higher systemic bioavailability of intranasal fentanyl spray compared to oral transmucosal fentanyl citrate in healthy subjects

(2013) Ruediger Nave et al.   DRUG DELIVERY

Subanalgesic ketamine enhances morphine-induced antinociceptive activity without cortical dysfunction in rats

(2013) Hiroki Shikanai et al.   Journal of Anesthesia

Appraisal of molecular tailoring approach for large clusters

(2013) Nityananda Sahu et al.   JOURNAL OF CHEMICAL PHYSICS

Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method for Full Quantum Mechanical Calculation of Protein Energy

(2013) Xianwei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

The role of the hippocampo-prefrontal cortex system in phencyclidine-induced psychosis: A model for schizophrenia

(2013) Eiichi Jodo   JOURNAL OF PHYSIOLOGY-PARIS

The critical effect of polarization on the dynamical structure of guanine quadruplex DNA

(2013) Jianing Song et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Involvement of the N-methyl-d-aspartate receptor GluN2D subunit in phencyclidine-induced motor impairment, gene expression, and increased Fos immunoreactivity

(2013) Hideko Yamamoto et al.   Molecular Brain

Differences between opioids: pharmacological, experimental, clinical and economical perspectives

(2012) Asbjørn M. Drewes et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

Observations on the Metabolism of Morphine to Hydromorphone in Pain Patients

(2012) M. M. Hughes et al.   JOURNAL OF ANALYTICAL TOXICOLOGY

Comparative clinical effects of hydromorphone and morphine: a meta-analysis

(2011) L. Felden et al.   BRITISH JOURNAL OF ANAESTHESIA

Adverse Effects in Hospice Patients with Chronic Kidney Disease Receiving Hydromorphone

(2011) Gobi Paramanandam et al.   JOURNAL OF PALLIATIVE MEDICINE

Cucurbituril chemistry: a tale of supramolecular success

(2011) Eric Masson et al.   RSC Advances

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Neurotoxicity of heroin–cocaine combinations in rat cortical neurons

(2010) Teresa Cunha-Oliveira et al.   TOXICOLOGY

Recent Developments in the Methods and Applications of the Bond Valence Model

(2009) Ian David Brown   CHEMICAL REVIEWS

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

Protonation of the Proximal Histidine Ligand in Heme Peroxidases

(2008) Jimmy Heimdal 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

Thermodynamics of stacking interactions in proteins

(2008) Simone Marsili et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Highly Efficient Cucurbit[8]uril-Templated Intramolecular Photocycloaddition of 2-Naphthalene-Labeled Poly(ethylene glycol) in Aqueous Solution

(2007) Xiao-Ling Wu et al.   JOURNAL OF ORGANIC CHEMISTRY