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37 results in Keywords: binding free energy

Theoretical and Computational Chemistry

Working Paper

Predictions of the poses and affinity of a ligand over the entire surface of a NEET protein: the case of human mitoNEET

Ke Zuo, Riccardo Capelli, Giulia Rossetti, Rachel Nechushtai, Paolo Carloni

Version 1 posted 10 October 2022

146

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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

680

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Theoretical and Computational Chemistry

Working Paper

Optimal Designs of Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability

Qingyi Yang, Woodrow W. Burchett, Gregory S. Steeno, David L. Mobley, Xinjun Hou

Version 2 posted 02 May 2019

928

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Theoretical and Computational Chemistry

Working Paper

Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

Bahaa Jawad, Puja Adhikari, Rudolf Podgornik, Wai-Yim Ching

Version 1 posted 19 May 2021

601

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Theoretical and Computational Chemistry

Working Paper

Predicting the Potential Effect of E484K Mutation on the Binding of 28 Antibodies to the Spike Protein of SARS-CoV-2 by Molecular Dynamics Simulation and Free Energy Calculation

Leyun Wu, Cheng Peng, Zhijian Xu, weiliang zhu

Version 1 posted 11 February 2021

691

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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

1,031

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Biological and Medicinal Chemistry

Working Paper

Binding and Reactivity of a Nitrile Oral Inhibitor of SARS-CoV-2 Main Protease Revealed by Computational Simulations

Carlos A. Ramos-Guzmán, Jose Javier Ruiz-Pernía, Iñaki Tuñón

Version 1 posted 23 July 2021

855

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Theoretical and Computational Chemistry

Working Paper

Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

Lovika Mittal, Anita Kumari, Mitul Srivastava, Mrityunjay Singh, Shailendra Asthana

Version 2 posted 10 April 2020

1,921

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Citations

Theoretical and Computational Chemistry

Working Paper

Dissociation pathways of the p53 DNA binding domain from DNA and critical roles of key residues elucidated by dPaCS-MD/MSM

Mohamed Sobeh, Akio kitao

Version 1 posted 13 December 2021

249

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Theoretical and Computational Chemistry

Working Paper

Challenges Encountered Applying Equilibrium and Non-Equilibrium Binding Free Energy Calculations

Hannah Baumann, Vytautas Gapsys, Bert L. de Groot, David Mobley

Version 2 posted 13 April 2021

1,154

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37 results in binding free energy in Keywords: binding free energy

Predictions of the poses and affinity of a ligand over the entire surface of a NEET protein: the case of human mitoNEET

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

Optimal Designs of Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability

Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation

Predicting the Potential Effect of E484K Mutation on the Binding of 28 Antibodies to the Spike Protein of SARS-CoV-2 by Molecular Dynamics Simulation and Free Energy Calculation

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

Binding and Reactivity of a Nitrile Oral Inhibitor of SARS-CoV-2 Main Protease Revealed by Computational Simulations

Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

Dissociation pathways of the p53 DNA binding domain from DNA and critical roles of key residues elucidated by dPaCS-MD/MSM

Challenges Encountered Applying Equilibrium and Non-Equilibrium Binding Free Energy Calculations

37 results in Keywords: binding free energy