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Theoretical and Computational Chemistry

Working Paper

Omicron P132H of SARS-CoV-2 Mpro is an allosteric mutant involved in modulating the dynamics of catalytic site entry loop

Zahoor Ahmad Bhat, Mohd Muzammil Khan, Jawed Iqbal, Ayyub Rehman, Arumugam Madhumalar

Version 2 posted 18 May 2023

221

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Theoretical and Computational Chemistry

Working Paper

BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations

Germano Heinzelmann, David Huggins, Michael Gilson

Version 2 posted 22 February 2024

898

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Theoretical and Computational Chemistry

Working Paper

An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package

Felix Bänsch, Mirco Daniel, Harald Lanig, Christoph Steinbeck, Achim Zielesny

Version 1 posted 08 February 2024

196

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Theoretical and Computational Chemistry

Working Paper

Accelerating Fragment Based Drug Discovery using Grand Canonical Nonequilibrium Candidate Monte Carlo

William Poole, Marley Samways, Davide Branduardi, Richard Taylor, Marcel Verdonk, Jonathan Essex

Version 1 posted 30 September 2024

291

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Theoretical and Computational Chemistry

Working Paper

Assessing the Performance of Docking, FEP, and MM/GBSA Methods on a Series of KLK6 Inhibitors

Wemenes José Lima Silva, Renato Ferreira de Freitas

Version 1 posted 17 April 2023

409

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Biological and Medicinal Chemistry

Working Paper

Exploration of cryptic pockets using enhanced sampling along normal modes: A case study of KRAS G12D

Neha Vithani, She Zhang, Jeffrey P. Thompson, Lara A. Patel, Alex Demidov, Junchao Xia, Alexander Balaeff, Ahmet Mentes, Yelena A. Arnautova, Anna Kohlmann, J. David Lawson, Anthony Nicholls, A Geoffrey Skillman, David N. LeBard

Version 1 posted 05 August 2024

366

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Biological and Medicinal Chemistry

Working Paper

Structural Determinants of the Binding and Activation of Estrogen Receptor alpha by Phenolic Thieno[2,3-d]pyrimidines

Vamshi Sammeta, Brian Anderson, John Norris, Chad Torrice, Carstyn Joiner, Shubin Liu, Haoxi Li, Konstantin Popov, Sean Fanning, Donald McDonnell, Timothy Willson

Version 1 posted 03 July 2023

149

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Theoretical and Computational Chemistry

Working Paper

INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations

Vale Cofer-Shabica, Maximilian Menger, Qi Ou, Yihan Shao, Joseph Subotnik, Shirin Faraji

Version 1 posted 02 March 2022

187

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1

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Theoretical and Computational Chemistry

Working Paper

Structure and Dynamics of Adsorbed Dopamine on Solvated Carbon Nanotubes and in a CNT Groove

Qizhang Jia, B. Jill Venton, Kateri H. DuBay

Version 1 posted 04 May 2022

134

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Molecular Docking and Molecular Dynamics Simulation to Predict Inhibitors Against HIV Envelope 1 Protein

Mustafa Arif, Gaurav Sharma

Version 1 posted 10 April 2024

203

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54 results in UBDB, Electrostatic interaction energy, HIV protease, drug discovery, molecular dynamics in Keywords: UBDB, Electrostatic interaction energy, HIV protease, drug discovery, molecular dynamics

Omicron P132H of SARS-CoV-2 Mpro is an allosteric mutant involved in modulating the dynamics of catalytic site entry loop

BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations

An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package

Accelerating Fragment Based Drug Discovery using Grand Canonical Nonequilibrium Candidate Monte Carlo

Assessing the Performance of Docking, FEP, and MM/GBSA Methods on a Series of KLK6 Inhibitors

Exploration of cryptic pockets using enhanced sampling along normal modes: A case study of KRAS G12D

Structural Determinants of the Binding and Activation of Estrogen Receptor alpha by Phenolic Thieno[2,3-d]pyrimidines

INAQS, a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations

Structure and Dynamics of Adsorbed Dopamine on Solvated Carbon Nanotubes and in a CNT Groove

Molecular Docking and Molecular Dynamics Simulation to Predict Inhibitors Against HIV Envelope 1 Protein

54 results in Keywords: UBDB, Electrostatic interaction energy, HIV protease, drug discovery, molecular dynamics