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16 results in Keywords: protein-ligand binding

Theoretical and Computational Chemistry

Working Paper

Simulating Protein-Ligand Binding with Neural Network Potentials

Shae-Lynn Lahey, Christopher Rowley

Version 1 posted 29 November 2019

759

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Biological and Medicinal Chemistry

Working Paper

Equilibrium and Non-equilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations

Agastya Prakash Bhati, Shunzhou Wan, Peter V. Coveney

Version 3 posted 17 October 2024

429

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Theoretical and Computational Chemistry

Working Paper

Is the functional response of a receptor determined by the thermodynamics of ligand binding?

Martin Vögele, Bin W. Zhang, Jonas Kaindl, Lingle Wang

Version 2 posted 27 September 2023

1,171

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Theoretical and Computational Chemistry

Working Paper

How robust is the ligand binding transition state?

Samik Bose, Samuel Lotz, Indrajit Deb, Megan Shuck, Kin Sing Stephen Lee, Alex Dickson

Version 1 posted 14 August 2023

325

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Theoretical and Computational Chemistry

Working Paper

Encoding Protein-Ligand Interactions: Binding Affinity Prediction with Multigraph-based Modeling and Graph Convolutional Network

Nedra Mekni, Hosein Fooladi, Ugo Perricone, Thierry Langer

Version 2 posted 18 December 2023

537

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Citations

Theoretical and Computational Chemistry

Working Paper

Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy

Thomas Evangelidis, Ilektra-Chara Giassa,, Mario Lovrić

Version 2 posted 27 December 2022

342

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Biological and Medicinal Chemistry

Working Paper

Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning

Angela Lopez-del Rio, Alfons Nonell-Canals, David Vidal, Alexandre Perera-Lluna

Version 1 posted 27 September 2018

674

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Theoretical and Computational Chemistry

Working Paper

Enhancing hit discovery in virtual screening through accurate calculation of absolute protein-ligand binding free energies

Wei Chen, Di Cui, Steven V. Jerome, Mayako Michino, Eelke B. Lenselink, David Huggins, Alexandre Beautrait, Jeremie Vendome, Robert Abel, Richard A. Friesner, Lingle Wang

Version 3 posted 21 December 2022

4,006

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Citations

Theoretical and Computational Chemistry

Working Paper

Deep Protein-Ligand Binding Prediction Using Unsupervised Learned Representations

Paul Kim, Robin Winter, Djork-Arné Clevert

Version 1 posted 08 January 2020

1,762

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Citations

Theoretical and Computational Chemistry

Working Paper

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys

Version 2 posted 27 September 2021

1,426

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16 results in protein-ligand binding in Keywords: protein-ligand binding

Simulating Protein-Ligand Binding with Neural Network Potentials

Equilibrium and Non-equilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations

Is the functional response of a receptor determined by the thermodynamics of ligand binding?

How robust is the ligand binding transition state?

Encoding Protein-Ligand Interactions: Binding Affinity Prediction with Multigraph-based Modeling and Graph Convolutional Network

Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy

Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning

Enhancing hit discovery in virtual screening through accurate calculation of absolute protein-ligand binding free energies

Deep Protein-Ligand Binding Prediction Using Unsupervised Learned Representations

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

16 results in Keywords: protein-ligand binding