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Biological and Medicinal Chemistry

Working Paper

Learning Protein-Ligand Binding Affinity with Atomic Environment Vectors

Rocco Meli, Andrew Anighoro, Mike Bodkin, Garrett Morris, Philip Biggin

Version 1 posted 22 December 2020

842

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2

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Analytical Chemistry

Working Paper

Proximity Biosensor Assay for PROTAC Ternary Complex Analysis

Irene Ponzo, Alice Solda, Charlotte Crowe, Goran Dahl, Stefan Geschwindner, Alessio Ciulli, Ulrich Rant

Version 1 posted 06 March 2024

1,913

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Theoretical and Computational Chemistry

Working Paper

How to make machine learning scoring functions competitive with FEP

Matthew Warren, ísak Valsson, Charlotte Deane, Aniket Magarkar, Garrett Morris, Philip Biggin

Version 1 posted 24 June 2024

1,522

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Theoretical and Computational Chemistry

Working Paper

Tuning Potential Functions to Host–Guest Binding Data

Jeffry Setiadi, Simon Boothroyd, David Slochower, David Dotson, Matthew Thompson, Jeffrey Wagner, Lee-Ping Wang, Michael K. Gilson

Version 2 posted 14 December 2023

444

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Theoretical and Computational Chemistry

Working Paper

Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the 2nd –Generation Mining Minima Method

Michael K. Gilson, Lawrence E. Stewart, Michael J. Potter, Simon P. Webb

Version 3 posted 10 July 2024

669

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Biological and Medicinal Chemistry

Working Paper

Evaluating the use of absolute binding free energy in the fragment optimization process.

Irfan Alibay, Aniket Magarkar, Daniel Seeliger, Philip Biggin

Version 3 posted 02 February 2022

1,978

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Biological and Medicinal Chemistry

Working Paper

Host-Guest Systems for the SAMPL9 Blinded Prediction Challenge: Phenothiazine as a Privileged Scaffold for Binding to Cyclodextrins

Brenda Andrade, Ashley Chen, Michael K. Gilson

Version 3 posted 14 December 2023

344

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Biological and Medicinal Chemistry

Working Paper

Papyrus - A large scale curated dataset aimed at bioactivity predictions

Olivier J. M. Béquignon, Brandon J. Bongers, Willem Jespers, Ad P. IJzerman, Bob van de Water, Gerard J. P. van Westen

Version 1 posted 01 November 2021

1,413

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Docking-informed machine learning for kinome wide affinity prediction

Jordy Schifferstein, Andrius Bernatavicius, Antonius P.A. Janssen

Version 1 posted 03 April 2024

542

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Biological and Medicinal Chemistry

Working Paper

BindingDB in 2024: a FAIR Knowledgebase of Protein-Small Molecule Binding Data

Tiqing Liu, Linda Hwang, Stephen K Burley, Carmen I Nitsche, Christopher Southan, W. Patrick Walters, Michael K. Gilson

Version 1 posted 13 September 2024

349

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11 results in affinity in Keywords: affinity

Learning Protein-Ligand Binding Affinity with Atomic Environment Vectors

Proximity Biosensor Assay for PROTAC Ternary Complex Analysis

How to make machine learning scoring functions competitive with FEP

Tuning Potential Functions to Host–Guest Binding Data

Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the 2nd –Generation Mining Minima Method

Evaluating the use of absolute binding free energy in the fragment optimization process.

Host-Guest Systems for the SAMPL9 Blinded Prediction Challenge: Phenothiazine as a Privileged Scaffold for Binding to Cyclodextrins

Papyrus - A large scale curated dataset aimed at bioactivity predictions

Docking-informed machine learning for kinome wide affinity prediction

BindingDB in 2024: a FAIR Knowledgebase of Protein-Small Molecule Binding Data

11 results in Keywords: affinity