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A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery

Zhixiong Lin, Junjie Zou, Chunwang Peng, Shuai Liu, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang

Version 1 posted 16 October 2020

1,138

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1

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Theoretical and Computational Chemistry

Working Paper

A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding

Edward Miller, Robert Murphy, Daniel Sindhikara, Ken Borrelli, Matthew Grisewood, Fabio Ranalli, Steven Dixon, Steven Jerome, Nicholas Boyles, Tyler Day, Phani Ghanakota, Sayan Mondal, Salma B. Rafi, Dawn M. Troast, Robert Abel, Richard Friesner

Version 2 posted 16 December 2020

4,218

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1

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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

583

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1

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Biological and Medicinal Chemistry

Working Paper

Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening

Jordan E. Crivelli-Decker, Zane Beckwith, Gary Tom, Ly Le, Sheenam Khuttan, Romelia Salomon-Ferrer, Jackson Beall, Rafael Gomez-Bombarelli, Andrea Bortolato

Version 1 posted 22 December 2023

1,926

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3

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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

974

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Biological and Medicinal Chemistry

Working Paper

Quantifying Cooperativity Through Binding Free Energies in Molecular Glue Degraders

Balint Dudas, Christina Athanasiou, Juan Carlos Mobarec, Edina Rosta

Version 1 posted 28 October 2024

574

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Theoretical and Computational Chemistry

Working Paper

FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery

Pengfei Li, Tingting Pu, Ye Mei

Version 2 posted 20 February 2025

829

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Biological and Medicinal Chemistry

Working Paper

Accurate physics-based prediction of binding affinities of RNA and DNA targeting ligands

Ara M. Abramyan, Anna Bochicchio, Chuanjie Wu, Wolfgang Damm, David R. Langley, Devleena Shivakumar, Dmitry Lupyan, Lingle Wang, Edward Harder, Eliud O. Oloo

Version 2 posted 26 August 2024

711

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Biological and Medicinal Chemistry

Working Paper

Harnessing free energy calculations to achieve kinome-wide selectivity in drug discovery campaigns: Wee1 case study

Jennifer Knight, Anthony Clark, Jiashi Wang, Andrew Placzeck, Pieter Bos, Sathesh Bhat, Jeffrey Bell, Sarah Silvergleid, Wu Yin, Felicia Gray, Shaoxian Sun, Karen Akinsanya, Robert Abel, Aleksey Gerasyuto

Version 1 posted 20 August 2024

544

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Theoretical and Computational Chemistry

Working Paper

Encoding prior knowledge in ensemble refinement

Jürgen Köfinger, Gerhard Hummer

Version 3 posted 20 February 2024

424

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40 results in Free energy perturbation in Keywords: Free energy perturbation

A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery

A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding

Absolute Binding Free Energy Calculations for Buried Water Molecules

Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening

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

Quantifying Cooperativity Through Binding Free Energies in Molecular Glue Degraders

FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery

Accurate physics-based prediction of binding affinities of RNA and DNA targeting ligands

Harnessing free energy calculations to achieve kinome-wide selectivity in drug discovery campaigns: Wee1 case study

Encoding prior knowledge in ensemble refinement

40 results in Keywords: Free energy perturbation