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Materials Science

Working Paper

Molecular Dynamics Simulations of the “Breathing” Phase Transformation of MOF Nanocrystallites

Julian Keupp, Rochus Schmid

Version 1 posted 17 June 2019

1,101

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1

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Physical Chemistry

Working Paper

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

Yasemin Basdogan, John Keith

Version 1 posted 28 March 2018

552

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Theoretical and Computational Chemistry

Working Paper

Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

Irfan Alibay, Kepa K. Burusco, Neil J. Bruce, Richard A. Bryce

Version 1 posted 05 October 2017

433

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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

624

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1

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Theoretical and Computational Chemistry

Working Paper

The Permeation Mechanism of Cisplatin through a Dioleoylphosphocholine Bilayer

Lorena Ruano, Gustavo Cárdenas, Juan Jose Nogueira

Version 2 posted 19 February 2021

470

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Theoretical and Computational Chemistry

Working Paper

Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques

Sebastian Wingbermühle, Lars V. Schäfer

Version 3 posted 21 May 2020

1,289

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Theoretical and Computational Chemistry

Working Paper

On the Dye-Protein Interaction of TMR-Biocytin – Streptavidin Complex: Molecular Simulations and Time-Resolved Fluorescence Quenching

Jang Mok Yoo, Sujin Lee, Hahkjoon Kim, Young Min Rhee

Version 2 posted 01 December 2023

88

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Biological and Medicinal Chemistry

Working Paper

Virtual reality sampled pathways guide free energy calculation of protein-ligand binding

Helen Deeks, Kirill Zinovjev, Jonathan Barnoud, Adrian Mulholland, Marc van der Kamp, David Glowacki

Version 1 posted 19 April 2022

327

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Theoretical and Computational Chemistry

Working Paper

Optimization of an in silico protocol to characterize membrane PAINS

Pedro R. Magalhães, Pedro B. P. S. Reis, Diogo Vila-Viçosa, Miguel Machuqueiro, Bruno L. Victor

Version 1 posted 07 December 2021

178

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Theoretical and Computational Chemistry

Working Paper

Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration.

Antoniu Bjola, Matteo Salvalaglio

Version 2 posted 23 April 2024

224

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21 results in Umbrella Sampling in Keywords: Umbrella Sampling

Molecular Dynamics Simulations of the “Breathing” Phase Transformation of MOF Nanocrystallites

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

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

The Permeation Mechanism of Cisplatin through a Dioleoylphosphocholine Bilayer

Capturing the Flexibility of a Protein-Ligand Complex: Binding Free Energies from Different Enhanced Sampling Techniques

On the Dye-Protein Interaction of TMR-Biocytin – Streptavidin Complex: Molecular Simulations and Time-Resolved Fluorescence Quenching

Virtual reality sampled pathways guide free energy calculation of protein-ligand binding

Optimization of an in silico protocol to characterize membrane PAINS

Estimating Free Energy Surfaces and their Convergence from multiple, independent static and history-dependent biased molecular-dynamics simulations with Mean Force Integration.

21 results in Keywords: Umbrella Sampling