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

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

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

Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA

(2022) Rory M. Crean et al.   Journal of Chemical Information and Modeling

Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation

(2022) Abdul Basit et al.   Journal of Chemical Information and Modeling

SAMPL9 blind predictions using nonequilibrium alchemical approaches

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

Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA

(2022) Mei Qian Yau et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

More is simpler: Decomposition of ligand‐binding affinity for proteins being disordered

(2022) Xiaohui Wang et al.   PROTEIN SCIENCE

Ion Dynamics and Selectivity of Nav channels from Molecular Dynamics Simulation

(2021) Zhaoxi Sun et al.   CHEMICAL PHYSICS

Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling

(2021) Esra Boz et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

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

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

Data-Driven Langevin Modeling of Nonequilibrium Processes

(2021) Benjamin Lickert et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

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

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

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

(2020) Adam Pecina et al.   ChemPlusChem

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

Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations

(2020) Amina Abula et al.   Journal of Chemical Information and Modeling

Computational Insights into the Conformational Accessibility and Binding Strength of SARS-CoV-2 Spike Protein to Human Angiotensin-Converting Enzyme 2

(2020) Cheng Peng et al.   Journal of Physical Chemistry Letters

Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules

(2019) Dario Vassetti et al.   Journal of Chemical Theory and Computation

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

Understanding Aldose Reductase-Inhibitors interactions with free energy simulation

(2019) Zhaoxi Sun et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Probing the structure and electronic properties of beryllium doped boron clusters: A planar BeB16− cluster motif for metallo-borophene

(2019) Dongliang Kang et al.   Scientific Reports

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

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

(2018) Thomas Gaillard   Journal of Chemical Information and Modeling

Residue-specific free energy analysis in ligand bindings to JAK2

(2018) Yifan Zhou et al.   MOLECULAR PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

(2018) Huiyong Sun 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

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

Protein–Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems

(2018) Gergely Kohut et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

(2017) Zhaoxi Sun 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

Carbon dioxide interacting with rare gases: Insights from high-level ab initio calculations of polarizability and hyperpolarizability effects

(2016) Anastasios Haskopoulos et al.   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

Reformulating the entropic contribution in molecular docking scoring functions

(2016) Piero Procacci   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

MN15: A Kohn–Sham global-hybrid exchange–correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions

(2016) Haoyu S. Yu et al.   Chemical Science

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

(2016) Valentina Cappello et al.   Scientific Reports

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

(2015) Ramu Anandakrishnan et al.   BIOPHYSICAL JOURNAL

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

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations

(2015) Gül H. Zerze et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Diffusion of Hydration Water around Intrinsically Disordered Proteins

(2015) Pooja Rani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

(2013) Joseph W. Kaus et al.   Journal of Chemical Theory and Computation

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

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

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

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

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

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers

(2009) Qin Cai et al.   Journal of Chemical Theory and Computation

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

Systematic optimization of long-range corrected hybrid density functionals

(2008) Jeng-Da Chai et al.   JOURNAL OF CHEMICAL PHYSICS

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