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

Discovery of Novel Inhibitors of CDK2 Using Docking and Physics‐based Binding Free Energy Calculation

(2022) Lei Zheng et al.   Chemical Biology & Drug Design

Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes

(2022) Jianzhong Chen et al.   RSC Advances

SAMPL9 blind predictions using nonequilibrium alchemical approaches

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

Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation

(2022) Shailesh Kumar Panday et al.   ACS Omega

Drug Design by Pharmacophore and Virtual Screening Approach

(2022) Deborah Giordano et al.   Pharmaceuticals

Free-Energy Landscape Analysis of Protein-Ligand Binding: The Case of Human Glutathione Transferase A1

(2022) Adrien Nicolaï et al.   Applied Sciences-Basel

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

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

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

Thermodynamics of pillararene·guest complexation: blinded dataset for the SAMPL9 challenge

(2021) Chun-Lin Deng et al.   NEW JOURNAL OF CHEMISTRY

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

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities

(2020) Ercheng Wang et al.   Journal of Chemical Information and Modeling

SQM/COSMO Scoring Function: Reliable Quantum‐Mechanical Tool for Sampling and Ranking in Structure‐Based Drug Design

(2020) Adam Pecina et al.   ChemPlusChem

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

How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?

(2020) Dongxiao Hao et al.   Journal of Chemical Information and Modeling

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

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

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity

(2019) Nguyen Thanh Nguyen et al.   Journal of Chemical Information and Modeling

Cyclodextrins: structure, physicochemical properties and pharmaceutical applications

(2018) Phatsawee Jansook et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark

(2018) Thomas Gaillard   Journal of Chemical Information and Modeling

Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution

(2018) Julia Gebhardt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculate protein–ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3

(2018) Xibing He et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2018) Juan Zeng et al.   CURRENT MEDICINAL CHEMISTRY

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

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

Interaction Entropy for Computational Alanine Scanning

(2017) Yuna Yan et al.   Journal of Chemical Information and Modeling

Carboxylatopillar[n]arenes: a versatile class of water soluble synthetic receptors

(2017) Suvankar Dasgupta et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

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

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

Supramolecular Vesicles Based on Complex of Trp-Modified Pillar[5]arene and Galactose Derivative for Synergistic and Targeted Drug Delivery

(2016) Kui Yang et al.   CHEMISTRY OF MATERIALS

PBSA_E: A PBSA-Based Free Energy Estimator for Protein–Ligand Binding Affinity

(2016) Xiao Liu et al.   Journal of Chemical Information and Modeling

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

(2016) Inês C. M. Simões et al.   Journal of Chemical Information and Modeling

Reformulating the entropic contribution in molecular docking scoring functions

(2016) Piero Procacci   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Host-Guest Complexes of Carboxylated Pillar[ n ]arenes With Drugs

(2016) Nial J. Wheate et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

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

Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies ofF. tularensisenoyl-ACP reductase (FabI)

(2015) Pin-Chih Su et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Amino-Functionalized Pillar[5]arene

(2014) Nathan L. Strutt et al.   CHEMISTRY-A EUROPEAN JOURNAL

Controllable Fabrication of Various Supramolecular Nanostructures Based on Nonamphiphilic Azobenzene Derivatives and Pillar[6]arene

(2014) Shan Qin et al.   CHINESE JOURNAL OF CHEMISTRY

Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics

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

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

Water-Soluble Pillar[7]arene: Synthesis, pH-Controlled Complexation with Paraquat, and Application in Constructing Supramolecular Vesicles

(2014) Zhengtao Li et al.   ORGANIC LETTERS

Achiral guest-induced chiroptical changes of a planar-chiral pillar[5]arene containing one π-conjugated unit

(2013) Tomoki Ogoshi et al.   CHEMICAL COMMUNICATIONS

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Stereochemical inversion in difunctionalised pillar[5]arenes

(2013) Nathan L. Strutt et al.   SUPRAMOLECULAR CHEMISTRY

A cationic water-soluble pillar[6]arene: synthesis, host–guest properties, and self-assembly with amphiphilic guests in water

(2013) Yingjie Ma et al.   RSC Advances

Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: Comparison of chrysin and flavopiridol

(2012) Katerina E. Tsitsanou et al.   FOOD AND CHEMICAL TOXICOLOGY

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

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

Pillar[6]arene-Based Photoresponsive Host–Guest Complexation

(2012) Guocan Yu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Theoretical investigations on vibrational spectra of pillar[5]arene-bis(pyridinium) complexes

(2012) Swarada R. Peerannawar et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

A Molecular Mechanics Approach to Modeling Protein–Ligand Interactions: Relative Binding Affinities in Congeneric Series

(2011) Chaya Rapp et al.   Journal of Chemical Information and Modeling

Postprocessing of Docked Protein−Ligand Complexes Using Implicit Solvation Models

(2011) Anton Lindström et al.   Journal of Chemical Information and Modeling

Efficient synthesis of copillar[5]arenes and their host–guest properties with dibromoalkanes

(2011) Luzhi Liu et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Virtual screening using molecular simulations

(2011) Tianyi Yang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Synthesis of a pillar[5]arene dimer by co-oligomerization and its complexation with n-octyltrimethyl ammonium hexafluorophosphate

(2011) Binyuan Xia et al.   TETRAHEDRON LETTERS

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

SFCscore: Scoring functions for affinity prediction of protein-ligand complexes

(2008) Christoph A. Sotriffer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS