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Works (49)

Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors

Journal of Chemical Information and Modeling
2025-02-10 | Journal article
DOI: 10.1021/acs.jcim.4c02126
Contributors: Sourav Pal; Kellie D. Nance; Dirgha Raj Joshi; Stephen C. Kales; Lin Ye; Xin Hu; Khalida Shamim; Alexey V. Zakharov
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AI-driven drug discovery: identification and optimization of ALDH3A1 selective inhibitors with nanomolar activity

2024-11-01 | Preprint
DOI: 10.26434/chemrxiv-2024-5zxxm-v2
Contributors: Sankalp Jain; Adam Yasgar; Anu Dalal; Marissa Davies; Aleksandra Nilova; Natalia Martinez; Anton Simeonov; Ganesha Rai; Alexey Zakharov
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Cell-Based Covalent-Capture Deubiquitinase Assay for Inhibitor Discovery

ACS Pharmacology & Translational Science
2024-09-13 | Journal article
DOI: 10.1021/acsptsci.4c00331
Contributors: Megan N. Doleschal; Jenna Miller; Sankalp Jain; Alexey V. Zakharov; Ganesha Rai; Anton Simeonov; Bolormaa Baljinnyam; Zhihao Zhuang
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Small-Molecule Disruptors of the Interaction between Calcium- and Integrin-Binding Protein 1 and Integrin αIIbβ3 as Novel Antiplatelet Agents

ACS Pharmacology & Translational Science
2024-07-12 | Journal article
DOI: 10.1021/acsptsci.4c00026
Contributors: Kalyan Golla; Adam Yasgar; Voddarahally N. Manjuprasanna; Meghna U. Naik; Bolormaa Baljinnyam; Alexey V. Zakharov; Sankalp Jain; Ganesha Rai; Ajit Jadhav; Anton Simeonov et al.
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AI-driven drug discovery: identification and optimization of ALDH3A1 selective inhibitors with nanomolar activity

2024-02-27 | Preprint
DOI: 10.26434/chemrxiv-2024-5zxxm
Contributors: Sankalp Jain; Adam Yasgar; Anu Dalal; Marissa Davies; Aleksandra Nilova; Natalia Martinez; Anton Simeonov; Ganesha Rai; Alexey Zakharov
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Data from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.c.7056448
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Data from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.c.7056448.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

Cancer Immunology Research
2024-02-02 | Journal article
DOI: 10.1158/2326-6066.CIR-22-1023
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Data Legends from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132708.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Data Legends from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132708
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S1 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132705
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S1 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132705.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S2 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132702
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S2 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132702.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S3 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132699
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S3 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132699.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S4 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132696
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S4 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132696.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S5 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132693
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S5 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132693.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S6 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132690.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S6 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132690
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S7 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132687
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Figure S7 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132687.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 1 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132684.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 1 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132684
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 2 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132681
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 2 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132681.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 3 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132678
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 3 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132678.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 4 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132675
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 4 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132675.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 5 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132672
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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Supplementary Table 5 from RALDH1 Inhibition Shows Immunotherapeutic Efficacy in Hepatocellular Carcinoma

2024-02-02 | Preprint
DOI: 10.1158/2326-6066.25132672.v1
Contributors: Pengfei Yu; Shuwen Cao; Shyh-Ming Yang; Ganesha Rai; Natalia J. Martinez; Adam Yasgar; Alexey V. Zakharov; Anton Simeonov; William A. Molina Arocho; Graham P. Lobel et al.
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One size does not fit all: revising traditional paradigms for QSAR-based virtual screenings.

2023-12-26 | Preprint
DOI: 10.26434/chemrxiv-2023-9cw9v
Contributors: James Wellnitz; Sankalp Jain; Joshua Hochuli; Travis Maxfield; Eugene Muratov; Alexander Tropsha; Alexey Zakharov
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Lies and Liabilities: Computational Assessment of High-Throughput Screening Hits to Identify Artifact Compounds

Journal of Medicinal Chemistry
2023-09-28 | Journal article
DOI: 10.1021/acs.jmedchem.3c00482
Contributors: Vinicius M. Alves; Adam Yasgar; James Wellnitz; Ganesha Rai; Marielle Rath; Rodolpho C. Braga; Stephen J. Capuzzi; Anton Simeonov; Eugene N. Muratov; Alexey V. Zakharov et al.
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Venglustat Inhibits Protein N-Terminal Methyltransferase 1 in a Substrate-Competitive Manner

Journal of Medicinal Chemistry
2022-09-22 | Journal article
DOI: 10.1021/acs.jmedchem.2c01050
Contributors: Guangping Dong; Youchao Deng; Adam Yasgar; Ravi Yadav; Daniel Talley; Alexey V. Zakharov; Sankalp Jain; Ganesha Rai; Nicholas Noinaj; Anton Simeonov et al.
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Application of Temperature-Responsive HIS-Tag Fluorophores to Differential Scanning Fluorimetry Screening of Small Molecule Libraries

2022-08-31 | Preprint
DOI: 10.1101/2022.08.31.506021
Contributors: Michael H. Ronzetti; Bolormaa Baljinnyam; Zina Itkin; Sankalp Jain; Ganesha Rai; Alexey V. Zakharov; Utpal Pal; Anton Simeonov
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A Genome-Edited ERα-HiBiT Fusion Reporter Cell Line for the Identification of ERα Modulators Via High-Throughput Screening and CETSA

ASSAY and Drug Development Technologies
2021-12-01 | Journal article
DOI: 10.1089/adt.2021.059
Contributors: Hunter G. Larson; Alexey V. Zakharov; Sukumar Sarkar; Shyh-Ming Yang; Ganesha Rai; James M. Larner; Anton Simeonov; Natalia J. Martinez
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Deep learning identifies synergistic drug combinations for treating COVID-19

Proceedings of the National Academy of Sciences
2021-09-28 | Journal article
DOI: 10.1073/pnas.2105070118
Contributors: Wengong Jin; Jonathan M. Stokes; Richard T. Eastman; Zina Itkin; Alexey V. Zakharov; James J. Collins; Tommi S. Jaakkola; Regina Barzilay
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Cross-platform Bayesian optimization system for autonomous biological assay development

2021-06-23 | Other
DOI: 10.1101/2021.06.23.448246
Contributors: Sam Elder; Carleen Klumpp-Thomas; Adam Yasgar; Jameson Travers; Shayne Frebert; Kelli M. Wilson; Alexey V. Zakharov; Jayme L. Dahlin; Christoph Kreisbeck; Dennis Sheberla et al.
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Discovery of TMPRSS2 Inhibitors from Virtual Screening as a Potential Treatment of COVID-19

ACS Pharmacology & Translational Science
2021-06-11 | Journal article
DOI: 10.1021/acsptsci.0c00221
Contributors: Xin Hu; Jonathan H. Shrimp; Hui Guo; Miao Xu; Catherine Z. Chen; Wei Zhu; Alexey V. Zakharov; Sankalp Jain; Paul Shinn; Anton Simeonov et al.
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Small Molecule Inhibitors of Activation-Induced Deaminase Decrease Class Switch Recombination in B Cells

ACS Pharmacology & Translational Science
2021-06-11 | Journal article
DOI: 10.1021/acsptsci.1c00064
Contributors: Juan Alvarez-Gonzalez; Adam Yasgar; Robert W. Maul; Amanda E. Rieffer; Daniel J. Crawford; Daniel J. Salamango; Dorjbal Dorjsuren; Alexey V. Zakharov; Daniel J. Jansen; Ganesha Rai et al.
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Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods

Journal of Chemical Information and Modeling
2021-02-22 | Journal article
DOI: 10.1021/acs.jcim.0c01164
Contributors: Sankalp Jain; Vishal B. Siramshetty; Vinicius M. Alves; Eugene N. Muratov; Nicole Kleinstreuer; Alexander Tropsha; Marc C. Nicklaus; Anton Simeonov; Alexey V. Zakharov
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Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the “Big Data” Era

Journal of Chemical Information and Modeling
2020-12-28 | Journal article
DOI: 10.1021/acs.jcim.0c00884
Contributors: Vishal B. Siramshetty; Dac-Trung Nguyen; Natalia J. Martinez; Noel T. Southall; Anton Simeonov; Alexey V. Zakharov
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Optimization of High-Throughput Methyltransferase Assays for the Discovery of Small Molecule Inhibitors

ACS Combinatorial Science
2020-08-10 | Journal article
DOI: 10.1021/acscombsci.0c00077
Contributors: Guangping Dong; Adam Yasgar; Darrell L. Peterson; Alexey Zakharov; Daniel Talley; Ken Chih-Chien Cheng; Ajit Jadhav; Anton Simeonov; Rong Huang
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Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the ‘Big Data’ Era

2020-04-16 | Preprint
DOI: 10.26434/chemrxiv.12119040.v1
Contributors: Vishal Babu Siramshetty; Dac-Trung Nguyen; Natalia J. Martinez; Anton Simeonov; Noel T. Southall; Alexey Zakharov
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Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models

Journal of Chemical Information and Modeling
2019-11-25 | Journal article
DOI: 10.1021/acs.jcim.9b00526
Contributors: Alexey V. Zakharov; Tongan Zhao; Dac-Trung Nguyen; Tyler Peryea; Timothy Sheils; Adam Yasgar; Ruili Huang; Noel Southall; Anton Simeonov
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Rational Use of Heterogeneous Data in Quantitative Structure–Activity Relationship (QSAR) Modeling of Cyclooxygenase/Lipoxygenase Inhibitors

Journal of Chemical Information and Modeling
2019-02-25 | Journal article
DOI: 10.1021/acs.jcim.8b00617
Contributors: Alexey A. Lagunin; Athina Geronikaki; Phaedra Eleftheriou; Pavel V. Pogodin; Alexey V. Zakharov
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Peer review (28 reviews for 5 publications/grants)

Review activity for ACS omega. (2)
Review activity for ACS sustainable chemistry & engineering. (1)
Review activity for Chemical research in toxicology. (3)
Review activity for Journal of chemical information and modeling. (21)
Review activity for Nature machine intelligence. (1)
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