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Theoretical and Computational Chemistry

Working Paper

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

Lauren Nelson, Sofia Bariami, Chris Ringrose, Joshua Horton, Vadiraj Kurdekar, Antonia Mey, Julien Michel, Daniel Cole

Version 2 posted 19 April 2021

908

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Organic Chemistry

Working Paper

An Asymmetric Mechanism in a Symmetric Molecular Machine

Florian Blanc, Marco Cecchini

Version 1 posted 01 April 2020

619

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1

Citations

Theoretical and Computational Chemistry

Working Paper

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

Rodrigo Recabarren, Kirill Zinovjev, Iñaki Tuñón, Jans Alzate-Morales

Version 1 posted 01 July 2020

858

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Theoretical and Computational Chemistry

Working Paper

Ab initio calculations of free energy of activation at multiple electronic structure levels made affordable: An effective combination of perturbation theory and machine learning

Tomas Bucko, Monika Gešvandtnerová, Dario Rocca

Version 2 posted 02 July 2020

1,102

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Theoretical and Computational Chemistry

Working Paper

Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations

Md Fulbabu Sk, Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar

Version 1 posted 06 April 2020

1,111

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Physical Chemistry

Working Paper

Challenges of the Use of Atomistic Simulations to Predict Solubilities of Drug-like Molecules

Guilherme Duarte Ramos Matos, David Mobley

Version 1 posted 10 May 2018

746

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1

Citations

Physical Chemistry

Working Paper

Ab Initio Metadynamics Calculations of Dimethylamine for Probing pKb Variations in Bulk vs. Surface Environments

Sohag Biswas, Hyuna Kwon, Kelley Barsanti, Nanna Myllys, James N. Smith, Bryan Wong

Version 2 posted 03 November 2020

689

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Theoretical and Computational Chemistry

Working Paper

Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations

Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann, Michael M Henry, James RB Eastwood, Richard J Gowers

Version 1 posted 31 October 2023

278

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Theoretical and Computational Chemistry

Working Paper

QM/MM study of proton transport process in [FeFe] hydrogenase enzyme

Rakesh Puthenkalathil, Bernd Ensing

Version 1 posted 16 August 2021

350

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Theoretical and Computational Chemistry

Working Paper

Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo

Sukanya Sasmal, Samuel C. Gill, Nathan M. Lim, David Mobley

Version 1 posted 23 October 2019

915

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Refine Search

46 results in Free Energy Calculations in Keywords: Free Energy Calculations

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

An Asymmetric Mechanism in a Symmetric Molecular Machine

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

Ab initio calculations of free energy of activation at multiple electronic structure levels made affordable: An effective combination of perturbation theory and machine learning

Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations

Challenges of the Use of Atomistic Simulations to Predict Solubilities of Drug-like Molecules

Ab Initio Metadynamics Calculations of Dimethylamine for Probing pKb Variations in Bulk vs. Surface Environments

Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations

QM/MM study of proton transport process in [FeFe] hydrogenase enzyme

Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo

46 results in Keywords: Free Energy Calculations