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Estimation of ligand binding free energy using multi-eGO.

Bruno Stegani, Emanuele Scalone, Fran Bacic Toplek, Thomas Lohr, Stefano Gianni, Michele Vendruscolo, Riccardo Capelli, Carlo Camilloni

Version 1 posted 25 July 2024

384

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Theoretical and Computational Chemistry

Working Paper

On analytical corrections for restraints in absolute binding free energy calculations

Stefan Boresch

Version 3 posted 13 March 2024

614

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Theoretical and Computational Chemistry

Working Paper

OPLS5: Addition of Polarizability and Improved Treatment of Metals

Wolfgang Damm, Steven Dajnowicz, Delaram Ghoreishi, Yalun Yu, Karthik Ganeshan, Owen Madin, Benjamin Rudshteyn, Rui Hu, Meng Wu, Yi Shang, Steven Albanese, Yefen Zou, Min Ye, Zachary Johnson, Michael Trzoss, Salma Rafi, Kanishk Kapilashrami, Noureldin Saleh, Phani Ghanakota, Yan Zhang, Jared Sampson, Wei Chen, Lingle Wang, Markus Dahlgren, Ellery Russell, Abba Leffler, Robert Abel, Richard Friesner, Edward Harder

Version 1 posted 13 August 2024

957

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Membrane Permeation of Psychedelic Compounds

Vito Federico Palmisano, Claudio Agnorelli, Andrea Fagiolini, David Erritzoe, David Nutt, Shirin Faraji, Juan Jose Nogueira

Version 1 posted 31 October 2023

255

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Theoretical and Computational Chemistry

Working Paper

Tuning Potential Functions to Host–Guest Binding Data

Jeffry Setiadi, Simon Boothroyd, David Slochower, David Dotson, Matthew Thompson, Jeffrey Wagner, Lee-Ping Wang, Michael K. Gilson

Version 2 posted 14 December 2023

444

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Theoretical and Computational Chemistry

Working Paper

An Approach to Alchemical Binding Free-Energy Calculations Using Coupled Topologies

David Huggins

Version 1 posted 15 October 2018

887

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Bind3P: Optimization of a Water Model with Host-Guest Binding Data

Jian Yin, Niel M. Henriksen, Hari S. Muddana, Michael K. Gilson

Version 2 posted 02 April 2018

1,032

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Biological and Medicinal Chemistry

Working Paper

Possibility of HIV-1 Protease Inhibitors-Clinical Trial Drugs as Repurposed Drugs for SARSCoV-2 Main Protease: A Molecular Docking, Molecular Dynamics and Binding Free Energy Simulation Study

Ancy Iruthayaraj, Sivanandam Magudeeswaran, Kumaradhas Poomani

Version 1 posted 28 April 2020

689

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Biological and Medicinal Chemistry

Working Paper

Drug Repurposing of Allophenylnorstatine Containing HIV-Protease Inhibitors Against SARS-CoV-2 Mpro: Insights from Molecular Dynamics Simulations and Binding Free Energy Estimations

Jiban Jyoti Dash, Priyanka Purohit, Jules Tshishimbi Muya, Biswa Ranjan Meher

Version 1 posted 02 June 2020

819

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Theoretical and Computational Chemistry

Working Paper

Broadening the scope of binding free energy calculations using a Separated Topologies approach

Hannah M. Baumann, Eric Dybeck, Christopher Lee McClendon, Frank C. Pickard IV, Vytautas Gapsys, Laura Pérez-Benito, David F. Hahn, Gary Tresadern, Alan M. Mathiowetz, David L. Mobley

Version 1 posted 10 March 2023

932

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2

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Refine Search

38 results in Binding free energy in Keywords: Binding free energy

Estimation of ligand binding free energy using multi-eGO.

On analytical corrections for restraints in absolute binding free energy calculations

OPLS5: Addition of Polarizability and Improved Treatment of Metals

Membrane Permeation of Psychedelic Compounds

Tuning Potential Functions to Host–Guest Binding Data

An Approach to Alchemical Binding Free-Energy Calculations Using Coupled Topologies

Bind3P: Optimization of a Water Model with Host-Guest Binding Data

Possibility of HIV-1 Protease Inhibitors-Clinical Trial Drugs as Repurposed Drugs for SARSCoV-2 Main Protease: A Molecular Docking, Molecular Dynamics and Binding Free Energy Simulation Study

Drug Repurposing of Allophenylnorstatine Containing HIV-Protease Inhibitors Against SARS-CoV-2 Mpro: Insights from Molecular Dynamics Simulations and Binding Free Energy Estimations

Broadening the scope of binding free energy calculations using a Separated Topologies approach

38 results in Keywords: Binding free energy