Artem Cherkasov

56 papers A* 1C 1Misc 1Journal 51Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2. J. Chem. Inf. Model. Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl H. Arrowsmith, Alan Ashworth, Fuqiang Ban, Hartmut Beck, Kevin P. Bishop, Hugo J. Bohórquez, Albina Bolotokova, Marko Breznik, Irene Chau, Yu Chen, Artem Cherkasov, Wim Dehaen, Dennis Della Corte, Katrin Denzinger, Niklas Piet Doering, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Francesco Gentile, Elisa Gibson, Ozan Gökdemir, Anders Gunnarsson, Judith Guenther, John J. Irwin, Jan Halborg Jensen, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Ashley Hutchinson, Shubhangi Kandwal, Andrea Karlova, Kushal Koirala, Sergei Kotelnikov, Dima Kozakov, Juyong Lee, Soowon Lee, Uta F. Lessel, Sijie Liu, Xuefeng Liu, Peter Loppnau, Jens Meiler, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Tudor I. Oprea, Brooks Paige, Amit Pandit, Keunwan Park, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Rahul Ravichandran, Didier Rognan, Edina Rosta, Yogesh Sabnis, Thomas Scott, Almagul Seitova, Purshotam Sharma, François Sindt, Minghu Song, Casper Steinmann, Rick Stevens, Valerij Talagayev, Valentyna V. Tararina, Olga O. Tarkhanova, Damon Tingey, John F. Trant, Dakota Treleaven, Alexander Tropsha, W. Patrick Walters, Jude Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Shuangjia Zheng, James S. Fraser, Matthieu Schapira
2026	J	`jnl`	Design of Highly Potent Antibiofilm, Antimicrobial Peptides Using Explainable Artificial Intelligence. J. Chem. Inf. Model. Karina Pikalyova, Tagir Akhmetshin, Alexey A. Orlov, Evan F. Haney, Noushin Akhoundsadegh, Jiaying You, Robert E. W. Hancock, Dragos Horvath, Gilles Marcou, Artem Cherkasov, Alexandre Varnek
2025	J	`jnl`	Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities. J. Chem. Inf. Model. Filipp Gusev, Evgeny Gutkin, Francesco Gentile, Fuqiang Ban, S. Benjamin Koby, Fengling Li, Irene Chau, Suzanne Ackloo, Cheryl H. Arrowsmith, Albina Bolotokova, Pegah Ghiabi, Elisa Gibson, Levon Halabelian, Scott Houliston, Rachel J. Harding, Ashley Hutchinson, Peter Loppnau, Sumera Perveen, Almagul Seitova, Hong Zeng, Matthieu Schapira, Artem Cherkasov, Olexandr Isayev, Maria G. Kurnikova
2025	A*	`conf`	Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation. ICML Mohit Pandey, Gopeshh Subbaraj, Artem Cherkasov, Martin Ester, Emmanuel Bengio
2025	J	`jnl`	Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation. CoRR Mohit Pandey, Gopeshh Subbaraj, Artem Cherkasov, Martin Ester, Emmanuel Bengio
2025	J	`jnl`	Why Pool When You Can Flow? Active Learning with GFlowNets. CoRR Renfei Zhang, Mohit Pandey, Artem Cherkasov, Martin Ester
2024	J	`jnl`	CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. J. Chem. Inf. Model. Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, Jan Beránek, Francois Berenger, Albina Bolotokova, Guillaume Bret, Marko Breznik, Emanuele Carosati, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled M. Edwards, Merveille K. I. Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S. Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J. Irwin, Olexandr Isayev, Aleksandra Ivanova, Célien Jacquemard, Austin J. Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta F. Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J. Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel G. Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina E. M. Schindler, François Sindt, Vojtech Spiwok, Casper Steinmann, Rick L. Stevens, Valerij Talagayev, Damon Tingey, Oanh Vu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, Matthieu Schapira
2024	J	`jnl`	PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J. Chem. Inf. Model. Hazem Mslati, Francesco Gentile, Mohit Pandey, Fuqiang Ban, Artem Cherkasov
2024	J	`jnl`	TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Design. Trans. Mach. Learn. Res. Tony Shen, Seonghwan Seo, Grayson Lee, Mohit Pandey, Jason R. Smith, Artem Cherkasov, Woo Youn Kim, Martin Ester
2023	J	`jnl`	Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors. J. Chem. Inf. Model. Olivia Garland, Anh-Tien Ton, Shoeib Moradi, Jason R. Smith, Suzana Kovacic, Kurtis Ng, Mohit Pandey, Fuqiang Ban, Jaeyong Lee, Marija Vuckovic, Liam J. Worrall, Robert N. Young, Ralph Pantophlet, Natalie C. J. Strynadka, Artem Cherkasov
2023	J	`jnl`	PurificationDB: database of purification conditions for proteins. Database J. Biol. Databases Curation Olivia Garland, Mariia Radaeva, Mohit Pandey, Artem Cherkasov, Nada Lallous
2023	J	`jnl`	TacoGFN: Target Conditioned GFlowNet for Structure-Based Drug Design. CoRR Tony Shen, Mohit Pandey, Jason R. Smith, Artem Cherkasov, Martin Ester
2022	J	`jnl`	DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking). Bioinform. Jean Charle Yaacoub, James Gleave, Francesco Gentile, Abraham C. Stern, Artem Cherkasov
2022	J	`jnl`	The transformational role of GPU computing and deep learning in drug discovery. Nat. Mach. Intell. Mohit Pandey, Michael Fernández, Francesco Gentile, Olexandr Isayev, Alexander Tropsha, Abraham C. Stern, Artem Cherkasov
2021	J	`jnl`	COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19. J. Chem. Inf. Model. Daniel Robert Korn, Vera Pervitsky, Tesia M. Bobrowski, Vinicius M. Alves, Charles Schmitt, Chris Bizon, Nancy Baker, Rada Chirkova, Artem Cherkasov, Eugene N. Muratov, Alexander Tropsha
2021	J	`jnl`	Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns. J. Chem. Inf. Model. Hazem Mslati, Francesco Gentile, Carl Perez, Artem Cherkasov
2020	J	`jnl`	DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules. Bioinform. Godwin Woo, Michael Fernández, Michael Hsing, Nathan A. Lack, Ayse Derya Cavga, Artem Cherkasov
2020	J	`jnl`	The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J. Chem. Inf. Model. Mariia Radaeva, Xuesen Dong, Artem Cherkasov
2019	J	`jnl`	All SMILES VAE. CoRR Zaccary Alperstein, Artem Cherkasov, Jason Tyler Rolfe
2019	—	`conf`	Progressive Docking - Deep Learning Based Approach for Accelerated Virtual Screening. ICANN (Workshop) Vibudh Agrawal, Francesco Gentile, Michael Hsing, Fuqiang Ban, Artem Cherkasov
2019	J	`jnl`	Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. J. Chem. Inf. Model. Michael Fernández, Fuqiang Ban, Godwin Woo, Olexandr Isayev, Carl Perez, Valery Fokin, Alexander Tropsha, Artem Cherkasov
2018	J	`jnl`	PADME: A Deep Learning-based Framework for Drug-Target Interaction Prediction. CoRR Qingyuan Feng, Evgenia V. Dueva, Artem Cherkasov, Martin Ester
2018	J	`jnl`	Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images. J. Chem. Inf. Model. Michael Fernández, Fuqiang Ban, Godwin Woo, Michael Hsing, Takeshi Yamazaki, Eric Leblanc, Paul S. Rennie, William J. Welch, Artem Cherkasov
2017	J	`jnl`	Best Practices of Computer-Aided Drug Discovery: Lessons Learned from the Development of a Preclinical Candidate for Prostate Cancer with a New Mechanism of Action. J. Chem. Inf. Model. Fuqiang Ban, Kush Dalal, Huifang Li, Eric Leblanc, Paul S. Rennie, Artem Cherkasov
2017	J	`jnl`	SimBoost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines. J. Cheminformatics Tong He, Marten Heidemeyer, Fuqiang Ban, Artem Cherkasov, Martin Ester
2016	J	`jnl`	Cheminformatics Modeling of Adverse Drug Responses by Clinically Relevant Mutants of Human Androgen Receptor. J. Chem. Inf. Model. Naman Paul, Lavinia A. Carabet, Nada Lallous, Takeshi Yamazaki, Martin E. Gleave, Paul S. Rennie, Artem Cherkasov
2013	J	`jnl`	Identification of Novel Androgen Receptor Antagonists Using Structure- and Ligand-Based Methods. J. Chem. Inf. Model. Huifang Li, Xin Ren, Eric Leblanc, Kate Frewin, Paul S. Rennie, Artem Cherkasov
2012	J	`jnl`	Targeting protein-protein interactions using methods of cheminformatics. J. Cheminformatics Artem Cherkasov
2011	J	`jnl`	Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Comput. Aided Mol. Des. Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Christof H. Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko
2011	J	`jnl`	Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Cheminformatics Iurii Sushko, Anil Kumar Pandey, Sergii Novotarskyi, Robert Körner, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Yu. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria A. Grishina, Johann Gasteiger, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko
2010	J	`jnl`	Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Artem Cherkasov, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus-Robert Müller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Süleyman Cenk Sahinalp, Roberto Todeschini, Pavel G. Polishchuk, Anatoly G. Artemenko, Victor Kuzmin, Todd M. Martin, Douglas M. Young, Denis Fourches, Eugene N. Muratov, Alexander Tropsha, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexandre Varnek, Volodymyr V. Prokopenko, Igor V. Tetko
2010	J	`jnl`	Prediction of highly-connected 'hub'-proteins in protein interaction networks using QSAR. J. Cheminformatics Michael Hsing, Kendall G. Byler, Artem Cherkasov
2010	J	`jnl`	Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. J. Comput. Biol. Alexander Schönhuth, Raheleh Salari, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
2009	J	`jnl`	The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. J. Comput. Biol. Fereydoun Hormozdiari, Raheleh Salari, Michael Hsing, Alexander Schönhuth, Simon K. Chan, Süleyman Cenk Sahinalp, Artem Cherkasov
2008	J	`jnl`	Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. J. Chem. Inf. Model. Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko
2008	J	`jnl`	Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins. BMC Bioinform. Michael Hsing, Artem Cherkasov
2008	C	`conf`	The Relation between Indel Length and Functional Divergence: A Formal Study. WABI Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp
2008	J	`jnl`	The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. BMC Syst. Biol. Michael Hsing, Kendall G. Byler, Artem Cherkasov
2008	J	`jnl`	Using Molecular Docking, 3D-QSAR, and Cluster Analysis for Screening Structurally Diverse Data Sets of Pharmacological Interest. J. Chem. Inf. Model. Osvaldo Andrade Santos-Filho, Artem Cherkasov
2007	J	`jnl`	AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinform. Christopher D. Fjell, Robert E. W. Hancock, Artem Cherkasov
2007	Misc	`conf`	Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. Pacific Symposium on Biocomputing Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov
2007	J	`jnl`	Novel approaches for small biomolecule classification and structural similarity search. SIGKDD Explor. Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
2007	J	`jnl`	Relationship between insertion/deletion (indel) frequency of proteins and essentiality. BMC Bioinform. Simon K. Chan, Michael Hsing, Fereydoun Hormozdiari, Artem Cherkasov
2006	J	`jnl`	Can 'Bacterial-Metabolite-Likeness' Model Improve Odds of 'in Silico' Antibiotic Discovery?. J. Chem. Inf. Model. Artem Cherkasov
2006	J	`jnl`	Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. J. Chem. Inf. Model. Emre Karakoç, Süleyman Cenk Sahinalp, Artem Cherkasov
2006	—	`conf`	Distance based algorithms for small biomolecule classification and structural similarity search. ISMB (Supplement of Bioinformatics) Emre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp
2006	J	`jnl`	Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins. J. Bioinform. Comput. Biol. Yvonne Y. Li, Steven J. M. Jones, Artem Cherkasov
2005	J	`jnl`	'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand. J. Chem. Inf. Model. Artem Cherkasov, Zheng Shi, Yvonne Y. Li, Steven J. M. Jones, Magid Fallahi, Geoffrey L. Hammond
2004	J	`jnl`	An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinform. Artem Cherkasov, Steven J. M. Jones
2004	J	`jnl`	Modeling of cell signaling pathways in macrophages by semantic networks. BMC Bioinform. Michael Hsing, Joel L. Bellenson, Conor Shankey, Artem Cherkasov
2004	J	`jnl`	Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinform. Artem Cherkasov, Steven J. M. Jones
2004	J	`jnl`	Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. BMC Bioinform. Artem Cherkasov, Shannan J. Ho Sui, Robert C. Brunham, Steven J. M. Jones
2003	J	`jnl`	Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges. J. Chem. Inf. Comput. Sci. Artem Cherkasov
2000	J	`jnl`	A New Method for Estimation of Homolytic C-H Bond Dissociation Enthalpies. J. Chem. Inf. Comput. Sci. Artem Cherkasov, Mats Jonsson
1999	J	`jnl`	Substituent Effects on Thermochemical Properties of C-, N-, O-, and S-Centered Radicals. Physical Interpretation of Substituent Effects. J. Chem. Inf. Comput. Sci. Artem Cherkasov, Mats Jonsson
1998	J	`jnl`	Substituent Effects on Thermochemical Properties of Free Radicals. New Substituent Scales for C-Centered Radicals. J. Chem. Inf. Comput. Sci. Artem Cherkasov, Mats Jonsson