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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

328

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Catalysis

Working Paper

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases

Ewa Chudyk, Michael Beer, Michael A.L. Limb, Charlotte A. Jones, James Spencer, Mark W. van der Kamp, Adrian Mulholland

Version 1 posted 22 March 2022

308

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1

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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

194

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Theoretical and Computational Chemistry

Working Paper

OGRe: Optimal grid refinement protocol for accurate free energy surfaces and its application to proton hopping in zeolites and 2D COF stacking

Sander Borgmans, Sven M.J. Rogge, Louis Vanduyfhuys, Veronique Van Speybroeck

Version 1 posted 18 September 2023

193

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Theoretical and Computational Chemistry

Working Paper

Do all paths lead to Rome? How reliable is umbrella sampling along a single path?

Noora Aho, Gerrit Groenhof, Pavel Buslaev

Version 2 posted 23 May 2024

915

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Physical Chemistry

Working Paper

Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Aromatic Substrates through Phospholipid Bilayers

Sang Noh, Rebecca Notman

Version 3 posted 13 May 2020

1,658

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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

562

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Biological and Medicinal Chemistry

Working Paper

If You Cannot Win Them, Join Them: Understanding New Ways to Target STAT3 by Small Molecules

Francesc Sabanés, Joao Victor de Souza Cunha, Roger Estrada-Tejedor, Agnieszka K Bronowska

Version 1 posted 28 May 2019

614

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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

442

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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

1,346

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23 results in Umbrella sampling in Keywords: Umbrella sampling

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

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases

Optimization of an in silico protocol to characterize membrane PAINS

OGRe: Optimal grid refinement protocol for accurate free energy surfaces and its application to proton hopping in zeolites and 2D COF stacking

Do all paths lead to Rome? How reliable is umbrella sampling along a single path?

Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Aromatic Substrates through Phospholipid Bilayers

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

If You Cannot Win Them, Join Them: Understanding New Ways to Target STAT3 by Small Molecules

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

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

23 results in Keywords: Umbrella sampling