John Karanicolas

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 40

Top Topics

Pseudomonas Aeruginosa

Binding Protein

Top Venues

bioRxiv : the preprint server for biology

ACS chemical biology

Research square

Journal of medicinal chemistry

This page only lists publications with an associated author ORCID identifier.

Publications

Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Victoria Mischley, Johannes Maier, Jesse Chen, John Karanicolas
PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. bioRxiv : the preprint server for biology (2024)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology 19 (1) (2023)
Nan Bai, Yusuf Adeshina, Igor Bychkov, Yan Xia, Ragul Gowthaman, Sven A Miller, Abhishek K Gupta, David K Johnson, Lan Lan, Erica A Golemis, Petr B Makhov, Liang Xu, Manoj M Pillai, Yanis Boumber, John Karanicolas
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. bioRxiv : the preprint server for biology (2023)
Wern Juin Gabriel Ong, Palani Kirubakaran, John Karanicolas
Poor Generalization by Current Deep Learning Models for Predicting Binding Affinities of Kinase Inhibitors. bioRxiv : the preprint server for biology (2023)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology (2023)
Nan Bai, Yusuf Adeshina, Igor Bychkov, Yan Xia, Ragul Gowthaman, Sven A Miller, Abhishek Gupta, David K Johnson, Lan Lan, Erica A Golemis, Peter Makhov, Liang Xu, Manoj M Pillai, Yanis Boumber, John Karanicolas
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. Research square (2023)
Nan Bai, Yusuf Adeshina, Igor Bychkov, Yan Xia, Ragul Gowthaman, Sven A Miller, Abhishek Gupta, David K Johnson, Lan Lan, Erica A Golemis, Peter Makhov, Liang Xu, Manoj M Pillai, Yanis Boumber, John Karanicolas
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. Research square (2023)
Nan Bai, Yusuf Adeshina, Igor Bychkov, Yan Xia, Ragul Gowthaman, Sven A Miller, Abhishek K Gupta, David K Johnson, Lan Lan, Erica A Golemis, Petr B Makhov, Liang Xu, Manoj M Pillai, Yanis Boumber, John Karanicolas
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. bioRxiv : the preprint server for biology (2023)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology 19 (1) (2023)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology 19 (1) (2023)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology 19 (1) (2023)
Nan Bai, Yusuf Adeshina, Igor Bychkov, Yan Xia, Ragul Gowthaman, Sven A Miller, Abhishek Gupta, David K Johnson, Lan Lan, Erica A Golemis, Peter Makhov, Liang Xu, Manoj M Pillai, Yanis Boumber, John Karanicolas
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. Research square (2023)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology 19 (1) (2023)
Connor Quinn, Mario C Rico, Carmen Merali, Carlos A Barrero, Oscar Perez-Leal, Victoria Mischley, John Karanicolas, Scott L Friedman, Salim Merali
Secreted folate receptor γ drives fibrogenesis in metabolic dysfunction-associated steatohepatitis by amplifying TGFβ signaling in hepatic stellate cells. Science translational medicine 15 (715) (2023)
Naomi E Widstrom, Grigorii V Andrianov, Jason L Heier, Celina Heier, John Karanicolas, Laurie L Parker
Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling. ACS chemical biology 19 (1) (2023)
Nan Bai, Yusuf Adeshina, Igor Bychkov, Yan Xia, Ragul Gowthaman, Sven A Miller, Abhishek K Gupta, David K Johnson, Lan Lan, Erica A Golemis, Petr B Makhov, Liang Xu, Manoj M Pillai, Yanis Boumber, John Karanicolas
Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. bioRxiv : the preprint server for biology (2023)
Alexandra Indeglia, Jessica C Leung, Sven A Miller, Julia I-Ju Leu, James F Dougherty, Nicole L Clarke, Nicole A Kirven, Chunlei Shao, Lei Ke, Scott Lovell, Thibaut Barnoud, David Y Lu, Cindy Lin, Toshitha Kannan, Kevin P Battaile, Tyler Hong Loong Yang, Isabela Batista Oliva, Daniel T Claiborne, Peter Vogel, Lijun Liu, Jingjing Liu, Yulia Nefedova, Joel A Cassel, Noam Auslander, Andrew V Kossenkov, John Karanicolas, Maureen E Murphy
An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression. Cancer discovery (2023)
Savannah J Post, Colleen E Keohane, Lauren M Rossiter, Anna R Kaplan, Jittasak Khowsathit, Katie Matuska, John Karanicolas, William M Wuest
Correction to "Target-Based Design of Promysalin Analogs Identifies a New Putative Binding Cleft in Succinate Dehydrogenase". ACS infectious diseases 8 (7) (2022)
Melissa J Ruggiero, Shipra Malhotra, Aron W Fenton, Liskin Swint-Kruse, John Karanicolas, Bruno Hagenbuch
Structural Plasticity Is a Feature of Rheostat Positions in the Human Na + /Taurocholate Cotransporting Polypeptide (NTCP). International journal of molecular sciences 23 (6) (2022)
Grigorii V Andrianov, Wern Juin Gabriel Ong, Ilya Serebriiskii, John Karanicolas
Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging. Journal of chemical information and modeling (2021)
Nan Bai, Sven A Miller, Grigorii V Andrianov, Max C Yates, Palani Kirubakaran, John Karanicolas
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta. Journal of chemical information and modeling 61 (3) (2021)
Yusuf O Adeshina, Eric J Deeds, John Karanicolas
Machine learning classification can reduce false positives in structure-based virtual screening. Proceedings of the National Academy of Sciences of the United States of America 117 (31) (2020)
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F Alford, Melanie Aprahamian, Julien S Baker, Kyle A Barlow, Patrick Barth, Benjamin Basanta, Brian J Bender, Kristin Blacklock, Jaume Bonet, Scott E Boyken, Philip G Bradley, Chris Bystroff, Patrick Conway, Seth Cooper, Bruno E Correia, Brian Coventry, Rachel J Hagey, René M De Jong, Frank DiMaio, Lorna Dsilva, Roland L Dunbrack, Alexander S Ford, Brandon Frenz, Darwin Y Fu, Caleb Geniesse, Lukasz Goldschmidt, Ragul Gowthaman, Jeffrey J Gray, Dominik Gront, Sharon Guffy, Scott Horowitz, Po-Ssu Huang, Thomas Huber, Tim M Jacobs, Jeliazko R Jeliazkov, David K Johnson, Kalli Kappel, John Karanicolas, Hamed Khakzad, Karen R Khar, Sagar D Khare, Firas Khatib, Alisa Khramushin, Indigo C King, Robert Kleffner, Brian Koepnick, Tanja Kortemme, Georg Kuenze, Brian Kuhlman, Daisuke Kuroda, Jason W Labonte, Jason K Lai, Gideon Lapidoth, Andrew Leaver-Fay, Steffen Lindert, Thomas Linsky, Nir London, Joseph H Lubin, Sergey Lyskov, Jack Maguire, Lars Malmström, Enrique Marcos, Orly Marcu, Nicholas A Marze, Jens Meiler, Rocco Moretti, Vikram Khipple Mulligan, Santrupti Nerli, Christoffer Norn, Shane Ó'Conchúir, Noah Ollikainen, Sergey Ovchinnikov, Michael S Pacella, Xingjie Pan, Hahnbeom Park, Ryan E Pavlovicz, Manasi Pethe, Brian G Pierce, Kala Bharath Pilla, Barak Raveh, P Douglas Renfrew, Shourya S Roy Burman, Aliza Rubenstein, Marion F Sauer, Andreas Scheck, William R Schief, Ora Schueler-Furman, Yuval Sedan, Alexander M Sevy, Nikolaos G Sgourakis, Lei Shi, Justin B Siegel, Daniel-Adriano Silva, Shannon Smith, Yifan Song, Amelie Stein, Maria Szegedy, Frank D Teets, Summer B Thyme, Ray Yu-Ruei Wang, Andrew Watkins, Lior Zimmerman, Richard A Bonneau
Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature methods 17 (7) (2020)
Savannah J Post, Colleen E Keohane, Lauren M Rossiter, Anna R Kaplan, Jittasak Khowsathit, Katie Matuska, John Karanicolas, William M Wuest
Target-Based Design of Promysalin Analogues Identifies a New Putative Binding Cleft in Succinate Dehydrogenase. ACS infectious diseases 6 (6) (2020)
Xiaoqing Wu, Gulhumay Gardashova, Lan Lan, Shuang Han, Cuncong Zhong, Rebecca T Marquez, Lanjing Wei, Spencer Wood, Sudeshna Roy, Ragul Gowthaman, John Karanicolas, Philip Gao, Dan A Dixon, Danny R Welch, Ling Li, Min Ji, Jeffrey Aube, Liang Xu
Targeting the interaction between RNA-binding protein HuR and FOXQ1 suppresses breast cancer invasion and metastasis. Communications biology 3 (1) (2020)
Lan Lan, Jiajun Liu, Minli Xing, Amber R Smith, Jinan Wang, Xiaoqing Wu, Carl Appelman, Ke Li, Anuradha Roy, Ragul Gowthaman, John Karanicolas, Amber D Somoza, Clay C C Wang, Yinglong Miao, Roberto De Guzman, Berl R Oakley, Kristi L Neufeld, Liang Xu
Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction. Cancers 12 (8) (2020)
Daria Van Tyne, Abigail L Manson, Mark M Huycke, John Karanicolas, Ashlee M Earl, Michael S Gilmore
Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream. Science translational medicine 11 (487) (2020)
Sean W Reilly, Aladdin A Riad, Chia-Ju Hsieh, Kristoffer Sahlholm, Daniel A Jacome, Suzy Griffin, Michelle Taylor, Chi-Chang Weng, Kuiying Xu, Nathan Kirschner, Robert R Luedtke, Christopher Parry, Shipra Malhotra, John Karanicolas, Robert H Mach
Leveraging a Low-Affinity Diazaspiro Orthosteric Fragment to Reduce Dopamine D3 Receptor (D3R) Ligand Promiscuity across Highly Conserved Aminergic G-Protein-Coupled Receptors (GPCRs). Journal of medicinal chemistry 62 (10) (2019)
Nan Bai, Heinrich Roder, Alex Dickson, John Karanicolas
Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Scientific reports 9 (1) (2019)
Christine E Kaiser, Juan Pablo Rincon Pabon, Jittasak Khowsathit, M Paola Castaldi, Steven L Kazmirski, David D Weis, Andrew X Zhang, John Karanicolas
Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue. ACS synthetic biology 7 (4) (2018)
Colleen E Keohane, Andrew D Steele, Christian Fetzer, Jittasak Khowsathit, Daria Van Tyne, Lucile Moynié, Michael S Gilmore, John Karanicolas, Stephan A Sieber, William M Wuest
Promysalin Elicits Species-Selective Inhibition of Pseudomonas aeruginosa by Targeting Succinate Dehydrogenase. Journal of the American Chemical Society 140 (5) (2018)
Shipra Malhotra, John Karanicolas
Correction to When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode? Journal of medicinal chemistry 60 (13) (2017)
Andrea Bazzoli, John Karanicolas
"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics. Journal of computational chemistry 38 (16) (2017)
Shipra Malhotra, John Karanicolas
When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode? Journal of medicinal chemistry 60 (1) (2016)