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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

978

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1

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Theoretical and Computational Chemistry

Working Paper

A Deep Learning Based Scaffold Hopping Strategy for the Design of Kinase Inhibitors

Lizhao Hu, Yuyao Yang, Shuangjia Zheng, Jun Xu, Ting Ran, Hongming Chen

Version 1 posted 24 May 2021

705

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Polymer Science

Review

Editing of Polymer Backbones

Aleksandr Zhukhovitskiy, Rachael Ditzler, Andrew King, Sydney Towell, Maxim Ratushnyy

Version 1 posted 12 December 2022

1,230

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1

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Theoretical and Computational Chemistry

Working Paper

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold-hopping capability

Oliver Laufkötter, Noé Sturm, Jürgen Bajorath, Ola Engkvist, Hongming Chen

Version 1 posted 15 February 2019

641

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1

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Biological and Medicinal Chemistry

Working Paper

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

Junjie Zou, Zhipeng Li, Shuai Liu, Chunwang Peng, Dong Fang, Xiao Wan, Zhixiong Lin, Tai-Sung Lee, Daniel Raleigh, Mingjun Yang, Carlos Simmerling

Version 1 posted 04 March 2021

495

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1

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Theoretical and Computational Chemistry

Working Paper

Deep Scaffold Hopping with Multi-modal Transformer Neural Networks

Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang

Version 1 posted 28 September 2020

1,314

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4

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Biological and Medicinal Chemistry

Working Paper

Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes

benjamin eduful, Sean O'Byrne, Louisa Temme, Christopher R. M. Asquith, Yi Liang, Alfredo Picado, Joseph Pilotte, Carrow Wells, William Zuercher, Carolina Catta-Preta, Priscila Zonzini Ramos, André Santiago, rafael Counago, Christopher G Langendorf, Kevin Nay, Jonathan S Oakhill, Thomas L Pulliam, Chenchu Lin, Dominik Awad, Timothy M. Willson, Daniel E Frigo, John W. Scott, David Drewry

Version 1 posted 28 December 2020

427

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Theoretical and Computational Chemistry

Working Paper

Improved Scaffold Hopping in Ligand-based Virtual Screening Using Neural Representation Learning

Luka Stojanovic, Milos Popovic, Nebojsa Tijanic, Goran Rakocevic, Marko Kalinic

Version 2 posted 22 July 2020

1,179

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Organic Chemistry

Working Paper

CONCISE AND PRACTICAL AVENUES TO 5,5-SPIRO-α-PROLINES

Ievgenii Iermolenko, Artem Artemenko, Dmytro Vasko, Alina Shcherbyna, Oleksandr Datsenko, Eugeniy Ostapchuk, Dmitry Lega, Alexander Rozhenko, Dmytro Volochnyuk, Serhiy Ryabukhin

Version 1 posted 06 February 2024

141

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Biological and Medicinal Chemistry

Working Paper

PromptSMILES: Prompting for scaffold decoration and fragment linking in chemical language models

Morgan Thomas, Mazen Ahmad, Gary Tresadern, Gianni de Fabritiis

Version 1 posted 06 March 2024

501

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13 results in Scaffold hopping in Keywords: Scaffold hopping

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

A Deep Learning Based Scaffold Hopping Strategy for the Design of Kinase Inhibitors

Editing of Polymer Backbones

Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold-hopping capability

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

Deep Scaffold Hopping with Multi-modal Transformer Neural Networks

Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes

Improved Scaffold Hopping in Ligand-based Virtual Screening Using Neural Representation Learning

CONCISE AND PRACTICAL AVENUES TO 5,5-SPIRO-α-PROLINES

PromptSMILES: Prompting for scaffold decoration and fragment linking in chemical language models

13 results in Keywords: Scaffold hopping