Isayev Lab

Publications

Research output from the Isayev Lab, including journal articles, preprints, conference proceedings, and book chapters.

29 total publications
1 in 2025

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Crowdsourced mapping extends the target space of kinase inhibitors

Anna Cichonska, Balaguru Ravikumar, Robert J Allaway, Sungjoon Park, Fangping Wan, Olexandr Isayev, Shuya Li, Michael Mason, Andrew Lamb, Ziaurrehman Tanoli, Minji Jeon, Sunkyu Kim, Mariya Popova, Stephen Capuzzi, Jianyang Zeng, Kristen Dang, Gregory Koytiger, Jaewoo Kang, Carrow I. Wells, Timothy M. Willson, The IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, Tudor I. Oprea, Avner Schlessinger, David H. Drewry, Gustavo Stolovitzky, Krister Wennerberg, Justin Guinney, Tero Aittokallio

Unpublished (2020)

Preprint
DOI

Crowdsourced mapping of unexplored target space of kinase inhibitors

Anna Cichońska, Balaguru Ravikumar, Robert J. Allaway, Fangping Wan, Sungjoon Park, Olexandr Isayev, Shuya Li, Michael Mason, Andrew Lamb, Ziaurrehman Tanoli, Minji Jeon, Sunkyu Kim, Mariya Popova, Stephen Capuzzi, Jianyang Zeng, Kristen Dang, Gregory Koytiger, Jaewoo Kang, Carrow I. Wells, Timothy M. Willson, The IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium, User oselot, Mehmet Tan, Team N121, Chih-Han Huang, Edward S. C. Shih, Tsai-Min Chen, Chih-Hsun Wu, Wei-Quan Fang, Jhih-Yu Chen, Ming-Jing Hwang, Team Let_Data_Talk, Xiaokang Wang, Marouen Ben Guebila, Behrouz Shamsaei, Sourav Singh, User thinng, Thin Nguyen, Team KKT, Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen, Team Boun, Hakime Öztürk, Elif Ozkirimli, Arzucan Özgür, Team KinaseHunter, Hansaim Lim, Lei Xie, Team AmsterdamUMC-KU-team, Georgi K. Kanev, Albert J. Kooistra, Bart A. Westerman, Team DruginaseLearning, Panagiotis Terzopoulos, Konstantinos Ntagiantas, Christos Fotis, Leonidas Alexopoulos, Team KERMIT-LAB - Ghent University, Dimitri Boeckaerts, Michiel Stock, Bernard De Baets, Yves Briers, Team QED, Yunan Luo, Hailin Hu, Jian Peng, Team METU_EMBLEBI_CROssBAR, Tunca Dogan, Ahmet S. Rifaioglu, Heval Atas, Rengul Cetin Atalay, Volkan Atalay, Maria J. Martin, Team DMIS_DK, Minji Jeon, Junhyun Lee, Seongjun Yun, Bumsoo Kim, Buru Chang, Team AI Winter is Coming, Team hulab, Gábor Turu, Ádám Misák, Bence Szalai, László Hunyady, Team ML-Med, Matthias Lienhard, Paul Prasse, Ivo Bachmann, Julia Ganzlin, Gal Barel, Ralf Herwig, Team Prospectors, Davor Oršolić, Bono Lučić, Višnja Stepanić, Tomislav Šmuc, Challenge organizers, Tudor I. Oprea, Avner Schlessinger, David H. Drewry, Gustavo Stolovitzky, Krister Wennerberg, Justin Guinney, Tero Aittokallio

Nature Communications , Vol. 12, Issue 1, pp. 3307 (2021)

Article
DOI

A practical guide to machine learning interatomic potentials – Status and future

Ryan Jacobs, Dane Morgan, Siamak Attarian, Jun Meng, Chen Shen, Zhenghao Wu, Clare Yijia Xie, Julia H. Yang, Nongnuch Artrith, Ben Blaiszik, Gerbrand Ceder, Kamal Choudhary, Gabor Csanyi, Ekin Dogus Cubuk, Bowen Deng, Ralf Drautz, Xiang Fu, Jonathan Godwin, Vasant Honavar, Olexandr Isayev, Anders Johansson, Boris Kozinsky, Stefano Martiniani, Shyue Ping Ong, Igor Poltavsky, Kj Schmidt, So Takamoto, Aidan P. Thompson, Julia Westermayr, Brandon M. Wood

Current Opinion in Solid State and Materials Science , Vol. 35, pp. 101214 (2025)

Article
DOI

Simulation Intelligence: Towards a New Generation of Scientific Methods

Alexander Lavin, David Krakauer, Hector Zenil, Justin Gottschlich, Tim Mattson, Johann Brehmer, Anima Anandkumar, Sanjay Choudry, Kamil Rocki, Atılım Güneş Baydin, Carina Prunkl, Brooks Paige, Olexandr Isayev, Erik Peterson, Peter L. McMahon, Jakob Macke, Kyle Cranmer, Jiaxin Zhang, Haruko Wainwright, Adi Hanuka, Manuela Veloso, Samuel Assefa, Stephan Zheng, Avi Pfeffer

Unpublished (2022)

Preprint
DOI arXiv

A critical overview of computational approaches employed for COVID-19 drug discovery

Eugene N. Muratov, Rommie Amaro, Carolina H. Andrade, Nathan Brown, Sean Ekins, Denis Fourches, Olexandr Isayev, Dima Kozakov, José L. Medina-Franco, Kenneth M. Merz, Tudor I. Oprea, Vladimir Poroikov, Gisbert Schneider, Matthew H. Todd, Alexandre Varnek, David A. Winkler, Alexey V. Zakharov, Artem Cherkasov, Alexander Tropsha

Chemical Society Reviews , Vol. 50, Issue 16, pp. 9121-9151 (2021)

Article
DOI

A community effort in SARS‐CoV‐2 drug discovery

Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, Simon Olsson, Lluís Raich, Robin Winter, Hatice Gokcan, Filipp Gusev, Evgeny M. Gutkin, Olexandr Isayev, Maria G. Kurnikova, Chamali H. Narangoda, Roman Zubatyuk, Ivan P. Bosko, Konstantin V. Furs, Anna D. Karpenko, Yury V. Kornoushenko, Mikita Shuldau, Artsemi Yushkevich, Mohammed B. Benabderrahmane, Patrick Bousquet‐Melou, Ronan Bureau, Beatrice Charton, Bertrand C. Cirou, Gérard Gil, William J. Allen, Suman Sirimulla, Stanley Watowich, Nick Antonopoulos, Nikolaos Epitropakis, Agamemnon Krasoulis, Vassilis Pitsikalis, Stavros Theodorakis, Igor Kozlovskii, Anton Maliutin, Alexander Medvedev, Petr Popov, Mark Zaretckii, Hamid Eghbal‐Zadeh, Christina Halmich, Sepp Hochreiter, Andreas Mayr, Peter Ruch, Michael Widrich, Francois Berenger, Ashutosh Kumar, Yoshihiro Yamanishi, Kam Y. J. Zhang, Emmanuel Bengio, Yoshua Bengio, Moksh J. Jain, Maksym Korablyov, Cheng‐Hao Liu, Gilles Marcou, Enrico Glaab, Kelly Barnsley, Suhasini M. Iyengar, Mary Jo Ondrechen, V. Joachim Haupt, Florian Kaiser, Michael Schroeder, Luisa Pugliese, Simone Albani, Christina Athanasiou, Andrea Beccari, Paolo Carloni, Giulia D'Arrigo, Eleonora Gianquinto, Jonas Goßen, Anton Hanke, Benjamin P. Joseph, Daria B. Kokh, Sandra Kovachka, Candida Manelfi, Goutam Mukherjee, Abraham Muñiz‐Chicharro, Francesco Musiani, Ariane Nunes‐Alves, Giulia Paiardi, Giulia Rossetti, S. Kashif Sadiq, Francesca Spyrakis, Carmine Talarico, Alexandros Tsengenes, Rebecca C. Wade, Conner Copeland, Jeremiah Gaiser, Daniel R. Olson, Amitava Roy, Vishwesh Venkatraman, Travis J. Wheeler, Haribabu Arthanari, Klara Blaschitz, Marco Cespugli, Vedat Durmaz, Konstantin Fackeldey, Patrick D. Fischer, Christoph Gorgulla, Christian Gruber, Karl Gruber, Michael Hetmann, Jamie E. Kinney, Krishna M. Padmanabha Das, Shreya Pandita, Amit Singh, Georg Steinkellner, Guilhem Tesseyre, Gerhard Wagner, Zi‐Fu Wang, Ryan J. Yust, Dmitry S. Druzhilovskiy, Dmitry A. Filimonov, Pavel V. Pogodin, Vladimir Poroikov, Anastassia V. Rudik, Leonid A. Stolbov, Alexander V. Veselovsky, Maria De Rosa, Giada De Simone, Maria R. Gulotta, Jessica Lombino, Nedra Mekni, Ugo Perricone, Arturo Casini, Amanda Embree, D. Benjamin Gordon, David Lei, Katelin Pratt, Christopher A. Voigt, Kuang‐Yu Chen, Yves Jacob, Tim Krischuns, Pierre Lafaye, Agnès Zettor, M. Luis Rodríguez, Kris M. White, Daren Fearon, Frank Von Delft, Martin A. Walsh, Dragos Horvath, Charles L. Brooks, Babak Falsafi, Bryan Ford, Adolfo García‐Sastre, Sang Yup Lee, Nadia Naffakh, Alexandre Varnek, Günter Klambauer, Thomas M. Hermans

Molecular Informatics , Vol. 43, Issue 1, pp. e202300262 (2024)

Article
DOI