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Biological and Medicinal Chemistry

Working Paper

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

Zhaoxi Sun, John Z. H. Zhang

Version 1 posted 02 January 2020

647

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1

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Physical Chemistry

Working Paper

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

Xiaohui Wang, Zhaoxi Sun

Version 2 posted 21 March 2019

1,180

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Physical Chemistry

Working Paper

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

Zhaoxi Sun

Version 2 posted 27 July 2020

615

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Physical Chemistry

Working Paper

BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

Zhaoxi Sun, Zhirong Liu

Version 3 posted 30 March 2021

498

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Physical Chemistry

Working Paper

BAR-Based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape: From Semi-Empirical to Ab Initio

Zhaoxi Sun

Version 2 posted 23 September 2019

740

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Theoretical and Computational Chemistry

Working Paper

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Zhaoxi Sun, Qiaole He

Version 2 posted 04 October 2021

455

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Biological and Medicinal Chemistry

Working Paper

Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

Richard Van, Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul Agarwal, Bernard Brooks, Rakhi Rajan, Yihan Shao

Version 1 posted 04 October 2024

146

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Physical Chemistry

Working Paper

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

Zhaoxi Sun, Zhe Huai, Qiaole He, Zhirong Liu

Version 1 posted 20 July 2021

557

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Physical Chemistry

Working Paper

SAMPL6 Host-Guest Binding Affinities and Binding Poses from Spherical-Coordinates-Biased Simulations

Zhaoxi Sun, Qiaole He, Xiao Li, Zhengdan Zhu

Version 2 posted 21 January 2020

731

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Physical Chemistry

Working Paper

Effects of enzyme-ligand interactions on the photoisomerization of a light-regulated chemotherapeutic drug

Ruibin Liang, Amirhossein Bakhtiiari

Version 1 posted 25 January 2022

285

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10 results in Free energy simulation in Keywords: Free energy simulation

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

BAR-based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region

BAR-Based Multi-dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape: From Semi-Empirical to Ab Initio

Seeding the Multi-dimensional Nonequilibrium Pulling for Hamiltonian Variation: Indirect Nonequilibrium Free Energy Simulations at QM levels

Exploring CRISPR-Cas9 HNH-Domain Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

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

SAMPL6 Host-Guest Binding Affinities and Binding Poses from Spherical-Coordinates-Biased Simulations

Effects of enzyme-ligand interactions on the photoisomerization of a light-regulated chemotherapeutic drug

10 results in Keywords: Free energy simulation