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Theoretical and Computational Chemistry

Working Paper

Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results

Laura Shub, Magdalena Korczynska, Duncan F. Muir, Fang-Yu Lin, Alan M. Mathiowetz, Michael J. Keiser

Version 1 posted 10 December 2024

169

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Theoretical and Computational Chemistry

Working Paper

Fragment Pose Prediction Using Non-Equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations

Nathan M. Lim, Meghan Osato, Gregory L. Warren, David L. Mobley

Version 2 posted 12 November 2019

573

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Theoretical and Computational Chemistry

Working Paper

Structural Analysis of COVID-19 Main Protease and its Interaction with the Inhibitor N3

Tika Ram Lamichhane, Madhav Prasad Ghimire

Version 1 posted 01 June 2020

1,022

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1

Citations

Biological and Medicinal Chemistry

Working Paper

Prediction of Dissociation Constant in Protein-Ligand Interaction

Masatoshi Kawashima

Version 1 posted 05 March 2021

887

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Theoretical and Computational Chemistry

Working Paper

Dynamic docking in protein-ligand modeling

Gordon Chalmers

Version 1 posted 28 June 2022

396

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

Finlay Clark, Graeme Robb, Daniel Cole, Julien Michel

Version 2 posted 09 May 2023

895

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Theoretical and Computational Chemistry

Working Paper

SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes

Adam Pecina, Jindřich Fanfrlík, Martin Lepšík, Jan Řezáč

Version 1 posted 13 July 2023

1,030

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1

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Biological and Medicinal Chemistry

Review

Recent advances in studying Toll-like receptors with the use of computational methods

Maria Bzówka, Weronika Bagrowska, Artur Góra

Version 3 posted 14 March 2023

215

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Biological and Medicinal Chemistry

Working Paper

Elucidating the Multiple Roles of Hydration in Protein-Ligand Binding via Layerwise Relevance Propagation and Big Data Analytics

Markus Lill, Ying Yang, Amr Mahmoud, Matthew Masters

Version 1 posted 15 February 2019

774

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Biological and Medicinal Chemistry

Working Paper

Multiplexed Small Molecule Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis

Bo Cai, Casey Krusemark

Version 1 posted 08 April 2021

583

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Refine Search

19 results in protein-ligand interactions in Keywords: protein-ligand interactions

Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results

Fragment Pose Prediction Using Non-Equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations

Structural Analysis of COVID-19 Main Protease and its Interaction with the Inhibitor N3

Prediction of Dissociation Constant in Protein-Ligand Interaction

Dynamic docking in protein-ligand modeling

Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes

Recent advances in studying Toll-like receptors with the use of computational methods

Elucidating the Multiple Roles of Hydration in Protein-Ligand Binding via Layerwise Relevance Propagation and Big Data Analytics

Multiplexed Small Molecule Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis

19 results in Keywords: protein-ligand interactions