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Theoretical and Computational Chemistry

Working Paper

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Ido Ben-Shalom, Zhixiong Lin, Brian Radak, Charles Lin, Woody Sherman, Michael K. Gilson

Version 1 posted 20 July 2020

591

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1

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Biological and Medicinal Chemistry

Working Paper

Improving ΔΔG predictions with a multi-task convolutional Siamese Network

Andrew McNutt, David Koes

Version 1 posted 14 December 2021

644

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Theoretical and Computational Chemistry

Working Paper

Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach

Piero Procacci

Version 1 posted 22 February 2022

362

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Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,788

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2

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Theoretical and Computational Chemistry

Working Paper

Absolute Binding Free Energy Calculations for Buried Water Molecules

Yunhui Ge, Hannah Baumann, David Mobley

Version 2 posted 29 September 2022

539

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1

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Theoretical and Computational Chemistry

Working Paper

Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free Energy Calculations using Lambda Dynamics

E. Prabhu Raman, Thomas J. Paul, Ryan L. Hayes, Charles L. Brooks III

Version 1 posted 10 August 2020

602

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Theoretical and Computational Chemistry

Working Paper

Leveraging a separation of states method for relative binding free energy calculations in systems with trapped waters

Swapnil Wagle, Pascal Merz, Yunhui Ge, Christopher Bayly, David Mobley

Version 1 posted 03 September 2024

162

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7 results in relative binding free energy in Keywords: relative binding free energy

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Improving ΔΔG predictions with a multi-task convolutional Siamese Network

Relative binding free energy between chemically distant compounds using a bidirectional nonequilibrium approach

Validation of AMBER/GAFF for Relative Free Energy Calculations

Absolute Binding Free Energy Calculations for Buried Water Molecules

Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free Energy Calculations using Lambda Dynamics

Leveraging a separation of states method for relative binding free energy calculations in systems with trapped waters

7 results in Keywords: relative binding free energy