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35 results in Keywords: binding free energy

Theoretical and Computational Chemistry

Working Paper

Non-bonded force field parameters from MBIS partitioning of the molecular electron density improve CB7 host-guest affinity predictions

Duvan Gonzalez, Luis Macaya, Carlos Castillo-Orellana, Toon Verstraelen, Stefan Vogt-Geisse, Esteban Vöhringer-Martinez

Version 2 posted 27 May 2022

265

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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

134

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Biological and Medicinal Chemistry

Working Paper

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors Inhibitors

Shunzhou Wan, Agastya Bhati, David Wright, Ian Wall, Alan Graves, Darren Green, Peter Coveney

Version 2 posted 19 April 2022

243

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Theoretical and Computational Chemistry

Working Paper

Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta-calculated Properties

Matheus Ferraz, José Neto, Roberto Lins, Erico Teixeira

Version 1 posted 09 August 2022

682

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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

664

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Citations

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

566

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Theoretical and Computational Chemistry

Working Paper

Computational Estimation of Potential Inhibitors from the Known Drugs against the Main Protease of SARS-CoV-2

Nguyen Minh Tam, Pham Minh Quan, Nguyen Xuan Ha, Pham Cam Nam, Huong Thi Thu Phung

Version 1 posted 25 February 2021

386

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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

646

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Theoretical and Computational Chemistry

Working Paper

Characterization of the Binding Poses of Classical and Photoswitchable Psychedelics Interacting with 5-HT2AR

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

Version 1 posted 08 February 2023

372

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Theoretical and Computational Chemistry

Working Paper

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Xiao Liu, Lei Zheng, Chu Qin, Yalong Cong, John Z. H. Zhang, Zhaoxi Sun

Version 1 posted 27 February 2023

164

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35 results in binding free energy in Keywords: binding free energy

Non-bonded force field parameters from MBIS partitioning of the molecular electron density improve CB7 host-guest affinity predictions

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

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors Inhibitors

Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta-calculated Properties

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

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

Computational Estimation of Potential Inhibitors from the Known Drugs against the Main Protease of SARS-CoV-2

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

Characterization of the Binding Poses of Classical and Photoswitchable Psychedelics Interacting with 5-HT2AR

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

35 results in Keywords: binding free energy