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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

991

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1

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Theoretical and Computational Chemistry

Working Paper

Dynamic docking in protein-ligand modeling

Gordon Chalmers

Version 1 posted 28 June 2022

375

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1

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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

575

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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

207

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Biological and Medicinal Chemistry

Working Paper

NEQUIM Contact System (NCS): A tool for generation and analysis of protein-ligand interaction fingerprint

Andrelly Martins-José, Julio Lopes

Version 1 posted 12 April 2024

77

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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

3,499

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Theoretical and Computational Chemistry

Working Paper

Computational molecular modeling of Paxlovid binding

Gordon Chalmers

Version 1 posted 29 June 2022

216

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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

547

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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

824

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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

1,007

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1

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Refine Search

18 results in Protein-ligand interactions in Keywords: Protein-ligand interactions

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

Dynamic docking in protein-ligand modeling

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

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

NEQUIM Contact System (NCS): A tool for generation and analysis of protein-ligand interaction fingerprint

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

Computational molecular modeling of Paxlovid binding

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

Prediction of Dissociation Constant in Protein-Ligand Interaction

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

18 results in Keywords: Protein-ligand interactions