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Biological and Medicinal Chemistry

Working Paper

Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets

Agastya P. Bhati, Art Hoti, Andrew Potterton, Mateusz K. Bieniek, Peter V. Coveney

Version 3 posted 10 May 2023

485

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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

328

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Theoretical and Computational Chemistry

Working Paper

Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Agastya P Bhati, Peter V. Coveney

Version 2 posted 02 March 2022

522

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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

661

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Theoretical and Computational Chemistry

Working Paper

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

Lauren Nelson, Sofia Bariami, Chris Ringrose, Joshua Horton, Vadiraj Kurdekar, Antonia Mey, Julien Michel, Daniel Cole

Version 2 posted 19 April 2021

908

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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

1,409

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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

3,874

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3

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Theoretical and Computational Chemistry

Working Paper

Multi-task Proteochemometric Modelling

Anastasia Pentina, Djork-Arné Clevert

Version 1 posted 16 February 2022

602

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Theoretical and Computational Chemistry

Working Paper

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

Stefan Holderbach, Lukas Adam, Bhyravabhotla Jayaram, Rebecca Wade, Goutam Mukherjee

Version 2 posted 01 September 2020

887

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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

1,742

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1

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

Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets

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

Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

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

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

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

Multi-task Proteochemometric Modelling

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

Deep Protein-Ligand Binding Prediction Using Unsupervised Learned Representations

16 results in Keywords: Protein-ligand binding