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Theoretical and Computational Chemistry

Working Paper

How Do Microbial Metabolites Interact with Their Protein Targets?

Mario Astigarraga, Andrés Sánchez-Ruiz, Aminata Diop-Aw, Raquel Quintero, Gonzalo Colmenarejo

Version 1 posted 15 October 2024

90

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Physical Chemistry

Working Paper

One Touch Is All It Takes: the Supramolecular Interaction between Ubiquitin and Lanthanide Complexes Revisited by Paramagnetic NMR and Molecular Dynamics

Karen Dos Santos, Alessio Bartocci, Natacha Gillet, Sandrine Denis-Quanquin, Amandine Roux, Eugene Lin, Zeren Xu, Raphaël Finizola, Pauline Chedozeau, Xi Chen, Cédric Caradeuc, Mathieu Baudin, Gildas Bertho, François Riobé, Olivier Maury, Elise Dumont, Nicolas Giraud

Version 1 posted 19 January 2024

224

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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

1,031

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1

Citations

Biological and Medicinal Chemistry

Working Paper

CANDOCK: Chemical Atomic Network Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials

Jonathan Fine, Janez Konc, Ram Samudralal, Gaurav Chopra

Version 1 posted 15 October 2018

588

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1

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Biological and Medicinal Chemistry

Working Paper

Prediction of Dissociation Constant in Protein-Ligand Interaction

Masatoshi Kawashima

Version 1 posted 05 March 2021

888

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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

Computational molecular modeling of Paxlovid binding

Gordon Chalmers

Version 1 posted 29 June 2022

235

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Theoretical and Computational Chemistry

Working Paper

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

Samuel Gill, Nathan M. Lim, Patrick Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory Ross, John D. Chodera, David Mobley

Version 5 posted 23 February 2018

3,518

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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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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

216

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Refine Search

19 results in Protein-Ligand interactions in Keywords: Protein-Ligand interactions

How Do Microbial Metabolites Interact with Their Protein Targets?

One Touch Is All It Takes: the Supramolecular Interaction between Ubiquitin and Lanthanide Complexes Revisited by Paramagnetic NMR and Molecular Dynamics

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

CANDOCK: Chemical Atomic Network Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials

Prediction of Dissociation Constant in Protein-Ligand Interaction

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

Computational molecular modeling of Paxlovid binding

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo

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

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

19 results in Keywords: Protein-Ligand interactions