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Protein kinases  
PLOS Computational Biology  
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures

Noah B. Herrington, Yan Chak Li, David Stein, Gaurav Pandey, Avner Schlessinger

Research Article | published 24 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012302

Views: 2967Citations: 6Saves: 8 • Shares: 16

Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks

Georgi K. Kanev, Yaran Zhang, Albert J. Kooistra, Andreas Bender, Rob Leurs, David Bailey, Thomas Würdinger, Chris de Graaf, Iwan J. P. de Esch, Bart A. Westerman

Research Article | published 05 Sep 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011301

Views: 1959Citations: 7Saves: 23 • Shares: 6

Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning

Li Xie, Lei Xie

Research Article | published 17 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010974

Views: 1576Citations: 6Saves: 25 • Shares: 1

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases

Christian Degnbol Madsen, Jotun Hein, Christopher T. Workman

Research Article | published 22 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009414

Views: 1839Citations: 1Saves: 7 • Shares: 1

Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data

Brandon M. Invergo

Research Article | published 13 May 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010110

Views: 1437Citations: 2Saves: 5 • Shares: 4

Characterization and clustering of kinase isoform expression in metastatic melanoma

David O. Holland, Valer Gotea, Kevin Fedkenheuer, Sushil K. Jaiswal, Catherine Baugher, Hua Tan, Michael Fedkenheuer, Laura Elnitski

Research Article | published 13 May 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010065

Views: 1885Citations: 5Saves: 10 • Shares: 3

KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions

Bingjie Xue, Benjamin Jordan, Saqib Rizvi, Kristen M. Naegle

Research Article | published 08 Feb 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008681

Views: 2342Citations: 13Saves: 22 • Shares: 7

Predicting kinase inhibitors using bioactivity matrix derived informer sets

Huikun Zhang, Spencer S. Ericksen, Ching-pei Lee, Gene E. Ananiev, Nathan Wlodarchak, Peng Yu, Julie C. Mitchell, Anthony Gitter, Stephen J. Wright, F. Michael Hoffmann, Scott A. Wildman, Michael A. Newton

Research Article | published 05 Aug 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006813

Views: 14490Citations: 9Saves: 38 • Shares: 4

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

Ingoo Lee, Jongsoo Keum, Hojung Nam

Research Article | published 14 Jun 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007129

Views: 33182Citations: 463Saves: 318 • Shares: 19

Integrated computational and Drosophila cancer model platform captures previously unappreciated chemicals perturbing a kinase network

Peter M. U. Ung, Masahiro Sonoshita, Alex P. Scopton, Arvin C. Dar, Ross L. Cagan, Avner Schlessinger

Research Article | published 26 Apr 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006878

Views: 4024Citations: 10Saves: 35 • Shares: 17

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

Dheeraj Dube, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal, Surajit Sengupta

Research Article | published 15 Jan 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006665

Views: 4490Citations: 13Saves: 16 • Shares: 9

Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents

Sandra Giuliani, Arthur C. Silva, Joyce V. V. B. Borba, Pablo I. P. Ramos, Ross A. Paveley, Eugene N. Muratov, Carolina Horta Andrade, Nicholas Furnham

Research Article | published 22 Oct 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006515

Views: 5780Citations: 32Saves: 73 • Shares: 5

Recognition of sites of functional specialisation in all known eukaryotic protein kinase families

Raju Kalaivani, Raju Reema, Narayanaswamy Srinivasan

Research Article | published 13 Feb 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1005975

Views: 2624Citations: 4Saves: 25 • Shares: 5

Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors

Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio

Research Article | published 07 Aug 2017 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1005678

Views: 12634Citations: 110Saves: 132 • Shares: 20

Modelling of the cancer cell cycle as a tool for rational drug development: A systems pharmacology approach to cyclotherapy

Robert C. Jackson, Giovanni Y. Di Veroli, Siang-Boon Koh, Ian Goldlust, Frances M. Richards, Duncan I. Jodrell

Research Article | published 03 May 2017 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1005529

Views: 6828Citations: 10Saves: 54 • Shares: 11

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