Substituent Effects on Thermochemical Properties of Free Radicals. New Substituent Scales for C-Centered Radicals. - Artem Cherkasov; Mats Jonsson (J. Chem. Inf. Comput. Sci., 1998)

Substituent Effects on Thermochemical Properties of C-, N-, O-, and S-Centered Radicals. Physical Interpretation of Substituent Effects. - Artem Cherkasov; Mats Jonsson (J. Chem. Inf. Comput. Sci., 1999)

A New Method for Estimation of Homolytic C-H Bond Dissociation Enthalpies. - Artem Cherkasov; Mats Jonsson (J. Chem. Inf. Comput. Sci., 2000)

Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges. - Artem Cherkasov (J. Chem. Inf. Comput. Sci., 2003)

Structural characterization of genomes by large scale sequence-structure threading. - Artem Cherkasov; Steven J. M. Jones (BMC Bioinform., 2004)

An approach to large scale identification of non-obvious structural similarities between proteins. - Artem Cherkasov; Steven J. M. Jones (BMC Bioinform., 2004)

Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. - Artem Cherkasov; Shannan J. Ho Sui; Robert C. Brunham; Steven J. M. Jones (BMC Bioinform., 2004)

Modeling of cell signaling pathways in macrophages by semantic networks. - Michael Hsing; Joel L. Bellenson; Conor Shankey; Artem Cherkasov (BMC Bioinform., 2004)

'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand. - Artem Cherkasov; Zheng Shi; Yvonne Y. Li; Steven J. M. Jones; Magid Fallahi; Geoffrey L. Hammond (J. Chem. Inf. Model., 2005)

Distance based algorithms for small biomolecule classification and structural similarity search. - Emre Karakoç; Artem Cherkasov; Süleyman Cenk Sahinalp (ISMB (Supplement of Bioinformatics), 2006)

Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins. - Yvonne Y. Li; Steven J. M. Jones; Artem Cherkasov (J. Bioinform. Comput. Biol., 2006)

Can 'Bacterial-Metabolite-Likeness' Model Improve Odds of 'in Silico' Antibiotic Discovery?. - Artem Cherkasov (J. Chem. Inf. Model., 2006)

Comparative QSAR- and Fragments Distribution Analysis of Drugs, Druglikes, Metabolic Substances, and Antimicrobial Compounds. - Emre Karakoç; Süleyman Cenk Sahinalp; Artem Cherkasov (J. Chem. Inf. Model., 2006)

Comparative QSAR Analysis of Bacterial-, Fungalplant- and Human Metabolites. - Emre Karakoç; Süleyman Cenk Sahinalp; Artem Cherkasov (Pacific Symposium on Biocomputing, 2007)

AMPer: a database and an automated discovery tool for antimicrobial peptides. - Christopher D. Fjell; Robert E. W. Hancock; Artem Cherkasov (Bioinform., 2007)

Relationship between insertion/deletion (indel) frequency of proteins and essentiality. - Simon K. Chan; Michael Hsing; Fereydoun Hormozdiari; Artem Cherkasov (BMC Bioinform., 2007)

Novel approaches for small biomolecule classification and structural similarity search. - Emre Karakoç; Artem Cherkasov; Süleyman Cenk Sahinalp (SIGKDD Explor., 2007)

The Relation between Indel Length and Functional Divergence: A Formal Study. - Raheleh Salari; Alexander Schönhuth; Fereydoun Hormozdiari; Artem Cherkasov; Süleyman Cenk Sahinalp (WABI, 2008)

Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins. - Michael Hsing; Artem Cherkasov (BMC Bioinform., 2008)

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. - Michael Hsing; Kendall G. Byler; Artem Cherkasov (BMC Syst. Biol., 2008)

Using Molecular Docking, 3D-QSAR, and Cluster Analysis for Screening Structurally Diverse Data Sets of Pharmacological Interest. - Osvaldo Andrade Santos-Filho; Artem Cherkasov (J. Chem. Inf. Model., 2008)

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. - Hao Zhu 012; Alexander Tropsha; Denis Fourches; Alexandre Varnek; Ester Papa; Paola Gramatica; Tomas Öberg; Phuong Dao; Artem Cherkasov; Igor V. Tetko (J. Chem. Inf. Model., 2008)

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study. - Fereydoun Hormozdiari; Raheleh Salari; Michael Hsing; Alexander Schönhuth; Simon K. Chan; Süleyman Cenk Sahinalp; Artem Cherkasov (J. Comput. Biol., 2009)

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length. - Alexander Schönhuth; Raheleh Salari; Fereydoun Hormozdiari; Artem Cherkasov; Süleyman Cenk Sahinalp (J. Comput. Biol., 2010)

Prediction of highly-connected 'hub'-proteins in protein interaction networks using QSAR. - Michael Hsing; Kendall G. Byler; Artem Cherkasov (J. Cheminformatics, 2010)

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. - 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; et al. (J. Chem. Inf. Model., 2010)

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. - 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; et al. (J. Comput. Aided Mol. Des., 2011)

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. - 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; et al. (J. Cheminformatics, 2011)

Targeting protein-protein interactions using methods of cheminformatics. - Artem Cherkasov (J. Cheminformatics, 2012)

Identification of Novel Androgen Receptor Antagonists Using Structure- and Ligand-Based Methods. - Huifang Li; Xin Ren; Eric Leblanc; Kate Frewin; Paul S. Rennie; Artem Cherkasov (J. Chem. Inf. Model., 2013)

Cheminformatics Modeling of Adverse Drug Responses by Clinically Relevant Mutants of Human Androgen Receptor. - Naman Paul; Lavinia A. Carabet; Nada Lallous; Takeshi Yamazaki; Martin E. Gleave; Paul S. Rennie; Artem Cherkasov (J. Chem. Inf. Model., 2016)

SimBoost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines. - Tong He; Marten Heidemeyer; Fuqiang Ban; Artem Cherkasov; Martin Ester (J. Cheminformatics, 2017)

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. - Fuqiang Ban; Kush Dalal; Huifang Li; Eric Leblanc; Paul S. Rennie; Artem Cherkasov (J. Chem. Inf. Model., 2017)

PADME: A Deep Learning-based Framework for Drug-Target Interaction Prediction. - Qingyuan Feng; Evgenia V. Dueva; Artem Cherkasov; Martin Ester (CoRR, 2018)

Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images. - Michael Fernández; Fuqiang Ban; Godwin Woo; Michael Hsing; Takeshi Yamazaki; Eric Leblanc; Paul S. Rennie; William J. Welch; Artem Cherkasov (J. Chem. Inf. Model., 2018)

Progressive Docking - Deep Learning Based Approach for Accelerated Virtual Screening. - Vibudh Agrawal; Francesco Gentile; Michael Hsing; Fuqiang Ban; Artem Cherkasov (ICANN (Workshop), 2019)

All SMILES VAE. - Zaccary Alperstein; Artem Cherkasov; Jason Tyler Rolfe (CoRR, 2019)

Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. - Michael Fernández; Fuqiang Ban; Godwin Woo; Olexandr Isayev; Carl Perez; Valery Fokin; Alexander Tropsha; Artem Cherkasov (J. Chem. Inf. Model., 2019)

DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules. - Godwin Woo; Michael Fernández; Michael Hsing; Nathan A. Lack; Ayse Derya Cavga; Artem Cherkasov (Bioinform., 2020)

The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. - Mariia Radaeva; Xuesen Dong; Artem Cherkasov (J. Chem. Inf. Model., 2020)

COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19. - Daniel Robert Korn; Vera Pervitsky; Tesia M. Bobrowski; Vinicius M. Alves; Charles Schmitt; Chris Bizon; Nancy Baker 001; Rada Chirkova; Artem Cherkasov; Eugene N. Muratov; Alexander Tropsha (J. Chem. Inf. Model., 2021)

Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns. - Hazem Mslati; Francesco Gentile; Carl Perez; Artem Cherkasov (J. Chem. Inf. Model., 2021)

DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking). - Jean Charle Yaacoub; James Gleave; Francesco Gentile; Abraham C. Stern; Artem Cherkasov (Bioinform., 2022)

The transformational role of GPU computing and deep learning in drug discovery. - Mohit Pandey; Michael Fernández; Francesco Gentile; Olexandr Isayev; Alexander Tropsha; Abraham C. Stern; Artem Cherkasov (Nat. Mach. Intell., 2022)

PurificationDB: database of purification conditions for proteins. - Olivia Garland; Mariia Radaeva; Mohit Pandey; Artem Cherkasov; Nada Lallous (Database J. Biol. Databases Curation, 2023)

TacoGFN: Target Conditioned GFlowNet for Structure-Based Drug Design. - Tony Shen; Mohit Pandey; Jason R. Smith 003; Artem Cherkasov; Martin Ester (CoRR, 2023)

Large-Scale Virtual Screening for the Discovery of SARS-CoV-2 Papain-like Protease (PLpro) Non-covalent Inhibitors. - Olivia Garland; Anh-Tien Ton; Shoeib Moradi; Jason R. Smith 003; Suzana Kovacic; Kurtis Ng; Mohit Pandey; Fuqiang Ban; Jaeyong Lee; Marija Vuckovic; Liam J. Worrall; Robert N. Young; et al. (J. Chem. Inf. Model., 2023)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - 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; et al. (J. Chem. Inf. Model., 2024)

PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. - Hazem Mslati; Francesco Gentile; Mohit Pandey; Fuqiang Ban; Artem Cherkasov (J. Chem. Inf. Model., 2024)

TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Design. - Tony Shen; Seonghwan Seo; Grayson Lee; Mohit Pandey; Jason R. Smith 003; Artem Cherkasov; Woo Youn Kim; Martin Ester (Trans. Mach. Learn. Res., 2024)

Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities. - 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; et al. (J. Chem. Inf. Model., 2025)

Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation. - Mohit Pandey; Gopeshh Subbaraj; Artem Cherkasov; Martin Ester; Emmanuel Bengio (CoRR, 2025)