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molecular mechanics; drug discovery; bioinformatics, internal coordinate mechanics; homology modelin

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University of California San Diego: La Jolla, CA, US

2009-09-01 to present | Professor (Skaggs School of Pharmacy and Pharmaceutical Sciences)
Employment
Source: Self-asserted source
Ruben Abagyan

Works (28)

Efficient Generation of Conformer Ensembles Using Internal Coordinates and a Generative Directional Graph Convolution Neural Network

Journal of Chemical Theory and Computation
2024-05-14 | Journal article
DOI: 10.1021/acs.jctc.4c00280
Contributors: Eugene Raush; Ruben Abagyan; Maxim Totrov
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Crossref

Authors’ Response to Peer Reviews of “Thyroid Hyperplasia and Neoplasm Adverse Events Associated With Glucagon-Like Peptide-1 Receptor Agonists in the Food and Drug Administration Adverse Event Reporting System: Retrospective Analysis”

JMIRx Med
2024-05-01 | Journal article
DOI: 10.2196/58273
Contributors: Tigran Makunts; Haroutyun Joulfayan; Ruben Abagyan
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Crossref

Thyroid Hyperplasia and Neoplasm Adverse Events Associated With Glucagon-Like Peptide-1 Receptor Agonists in the Food and Drug Administration Adverse Event Reporting System: Retrospective Analysis

JMIRx Med
2024-05-01 | Journal article
DOI: 10.2196/55976
Contributors: Tigran Makunts; Haroutyun Joulfayan; Ruben Abagyan
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Crossref

Co-occurring infections in cancer patients treated with checkpoint inhibitors significantly increase the risk of immune related adverse events

2024-02-15 | Preprint
DOI: 10.1101/2024.02.14.24302840
Contributors: Tigran Makunts; Siranuysh Grabska; Hovakim Grabski; Ruben Abagyan
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Crossref

Thyroid hyperplasia and neoplasm adverse events associated with GLP-1 receptor agonists in FDA Adverse Event Reporting System

2023-11-24 | Preprint
DOI: 10.1101/2023.11.19.23298750
Contributors: Tigran Makunts; Haroutyun Joulfayan; Ruben Abagyan
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Crossref

High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds

PLOS ONE
2023-05-09 | Journal article
DOI: 10.1371/journal.pone.0280232
Contributors: Conall Sauvey; Jesús Valdés; Ittipat Meewan; Gretchen Ehrenkaufer; Jonathan Blevitt; Paul Jackson; Ruben Abagyan
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Crossref

Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules

Journal of Chemical Information and Modeling
2022-12-12 | Journal article
DOI: 10.1021/acs.jcim.2c00790
Contributors: Eugene Raush; Ruben Abagyan; Maxim Totrov
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Crossref

Control of Unsaturation in De Novo Fatty Acid Biosynthesis by FabA

Biochemistry
2022-04-05 | Journal article
DOI: 10.1021/acs.biochem.2c00094
Contributors: Thomas G. Bartholow; Terra Sztain; Megan A. Young; D. John Lee; Tony D. Davis; Ruben Abagyan; Michael D. Burkart
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Crossref

Allosteric inhibitors of Zika virus NS2B-NS3 protease targeting protease in super-open conformation

2022-03-11 | Preprint
DOI: 10.1101/2022.03.09.483711
Contributors: Ittipat Meewan; Sergey A. Shiryaev; Chun-Teng Huang; Yi-Wen Lin; Chiao-Han Chuang; Alexey V. Terskikh; Ruben Abagyan
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Crossref

Mapping the gene network landscape of Alzheimer’s disease through integrating genomics and transcriptomics

PLOS Computational Biology
2022-02-25 | Journal article
DOI: 10.1371/journal.pcbi.1009903
Contributors: Sara Brin Rosenthal; Feixiong Cheng; Hao Wang; Da Shi; Cin Liu; Ruben Abagyan; Linda K. McEvoy; Chi-Hua Chen
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Crossref

Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events

PLOS ONE
2022-02-10 | Journal article
DOI: 10.1371/journal.pone.0263402
Contributors: Tigran Makunts; Yoshihiko Hirohashi; Keith Burkhart; Ruben Abagyan; Peter Lee
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Crossref

Structure based design and synthesis of novel Toll-like Receptor 2 (TLR 2) lipid antagonists

Bioorganic & Medicinal Chemistry Letters
2021-05 | Journal article
DOI: 10.1016/j.bmcl.2021.127861
Contributors: Srinivasa Reddy Natala; Agata Habas; Emily M. Stocking; Andrew Orry; Diana L. Price; Martin B. Gill; Douglas W. Bonhaus; Ruben Abagyan; Wolfgang Wrasidlo
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Crossref

Mtor inhibitors associated with higher cardiovascular adverse events—A large population database analysis

Clinical Transplantation
2021-04 | Journal article
DOI: 10.1111/ctr.14228
Contributors: Vi N. Nguyen; Ruben Abagyan; Shirley M. Tsunoda
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Crossref

Antineoplastic kinase inhibitors: A new class of potent anti-amoebic compounds

PLOS Neglected Tropical Diseases
2021-02-08 | Journal article
DOI: 10.1371/journal.pntd.0008425
Contributors: Conall Sauvey; Kiyoshi Kita; Gretchen Ehrenkaufer; Da Shi; Anjan Debnath; Ruben Abagyan
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Crossref

HMG-CoA Reductase Inhibitors as Drug Leads against Naegleria fowleri

ACS Chemical Neuroscience
2020-10-07 | Journal article
DOI: 10.1021/acschemneuro.0c00428
Contributors: Hye Jee Hahn; Ruben Abagyan; Larissa M. Podust; Shantanu Roy; Ibne Karim M. Ali; Anjan Debnath
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Crossref

Variable association of atypical femur fracture and osteonecrosis of jaw with bisphosphonates and denosumab use: Drug-safety surveillance study

2020-06-17 | Other
DOI: 10.1101/2020.06.15.20132290
Contributors: Tigran Makunts; Lara S. Anwar; Ruben Abagyan
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Crossref

Antineoplastic kinase inhibitors: a new class of potent anti-amoebic compounds Antineoplastic kinase inhibitors againstEntamoeba histolytica

2020-05-28 | Preprint
DOI: 10.1101/2020.05.28.120923
Contributors: Conall Sauvey; Gretchen Ehrenkaufer; Da Shi; Anjan Debnath; Ruben Abagyan
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Crossref

Determinants of cardiac adverse events of chloroquine and hydroxychloroquine in 20 years of drug safety surveillance reports

2020-05-26 | Other
DOI: 10.1101/2020.05.19.20107227
Contributors: Isaac V. Cohen; Tigran Makunts; Talar Moumedjian; Masara Issa; Ruben Abagyan
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Crossref

Druggable exosites of the human kino-pocketome

Journal of Computer-Aided Molecular Design
2020-03-10 | Journal article
DOI: 10.1007/s10822-019-00276-y
Contributors: George Nicola; Irina Kufareva; Andrey V. Ilatovskiy; Ruben Abagyan
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Crossref

Identification of Four Amoebicidal Nontoxic Compounds by a Molecular Docking Screen of Naegleria fowleri Sterol Δ8−Δ7-Isomerase and Phenotypic Assays

ACS Infectious Diseases
2019-12-13 | Journal article
DOI: 10.1021/acsinfecdis.9b00227
Contributors: Da Shi; Kirti Kandhwal Chahal; Patricia Oto; Louis-Felix Nothias; Anjan Debnath; James H. McKerrow; Larissa M. Podust; Ruben Abagyan
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Crossref

Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant

ACS Omega
2019-10-15 | Journal article
DOI: 10.1021/acsomega.9b02491
Contributors: Ittipat Meewan; Xingquan Zhang; Suchismita Roy; Carlo Ballatore; Anthony J. O’Donoghue; Robert T. Schooley; Ruben Abagyan
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Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma

PLOS ONE
2019-09-20 | Journal article
DOI: 10.1371/journal.pone.0214901
Contributors: Kirti Kandhwal Chahal; Chandrabose Karthikeyan; Jie Li; Irina Kufareva; Milind Parle; Donald L. Durden; Robert J. Wechsler-Reya; Clark C. Chen; Ruben Abagyan
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Crossref

Extended Multitarget Pharmacology of Anticancer Drugs

Journal of Chemical Information and Modeling
2019-06-24 | Journal article
DOI: 10.1021/acs.jcim.9b00031
Contributors: Da Shi; Feroz Khan; Ruben Abagyan
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Crossref

Nilotinib, an approved leukemia drug, inhibits Smoothened signaling in Hedgehog-dependent medulloblastoma

2019-03-25 | Other
DOI: 10.1101/588897
Contributors: Kirti K. Chahal; Jie Li; Irina Kufareva; Milind Parle; Donald L. Durden; Robert J. Wechsler-Reya; Clark C. Chen; Ruben Abagyan
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Crossref

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site

Journal of Medicinal Chemistry
2019-02-28 | Journal article
DOI: 10.1021/acs.jmedchem.8b01766
Contributors: Benoît Bestgen; Isabelle Krimm; Irina Kufareva; Ahmed Ashraf Moustafa Kamal; Wei-Guang Seetoh; Chris Abell; Rolf W. Hartmann; Ruben Abagyan; Claude Cochet; Marc Le Borgne et al.
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2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action

Journal of Medicinal Chemistry
2019-02-28 | Journal article
DOI: 10.1021/acs.jmedchem.8b01765
Contributors: Benoît Bestgen; Irina Kufareva; Weiguang Seetoh; Chris Abell; Rolf W. Hartmann; Ruben Abagyan; Marc Le Borgne; Odile Filhol; Claude Cochet; Thierry Lomberget et al.
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Crossref

Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells

ACS Omega
2018-09-30 | Journal article
DOI: 10.1021/acsomega.8b01864
Contributors: Kirti Kandhwal Chahal; Milind Parle; Ruben Abagyan
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Crossref

Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain

PLOS ONE
2018-04-18 | Journal article
DOI: 10.1371/journal.pone.0195521
Contributors: Tigran Makunts; Kenji Hashimoto; Isaac V. Cohen; Kelly C. Lee; Ruben Abagyan
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Peer review (3 reviews for 3 publications/grants)

Review activity for Journal of chemical theory and computation : (1)
Review activity for Nature cancer. (1)
Review activity for Nature communications (1)
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