Ruben Abagyan

Title(s)Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Addressing biomedical challenges with computational mechanics and big data
    NIH/NIGMS R35GM131881May 1, 2019 - Apr 30, 2024
    Role: Principal Investigator
    Structure, Dynamics and Activation Mechanisms of Chemokine Receptors
    NIH U01GM094612Sep 30, 2010 - Jun 30, 2015
    Role: Principal Investigator
    Novel Druggable Exosites in Protein Kinases
    NIH/NIGMS R01GM074832May 1, 2006 - Jul 31, 2009
    Role: Principal Investigator
    Flexible Macromolecular Docking
    NIH/NIGMS R01GM071872Aug 1, 2004 - May 31, 2018
    Role: Principal Investigator
    THEORETICAL PROTEIN STRUCTURE PREDICTION BY HOMOLGY
    NIH/NIGMS R01GM055418Sep 30, 1997 - Aug 31, 2002
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Co-Occurring Infections in Cancer Patients Treated with Checkpoint Inhibitors Significantly Increase the Risk of Immune-Related Adverse Events. Cancers (Basel). 2024 Aug 11; 16(16). Grabska S, Grabski H, Makunts T, Abagyan R. PMID: 39199593; PMCID: PMC11352782.
      View in: PubMed   Mentions:
    2. Hepatic injury and hepatic failure adverse events in 3,4-methylenedioxymethamphetamine users reported to the FDA Adverse Event Reporting System. Front Psychiatry. 2024; 15:1414622. Makunts T, Abagyan R. PMID: 38957734; PMCID: PMC11217510.
      View in: PubMed   Mentions:
    3. De novo generation of multi-target compounds using deep generative chemistry. Nat Commun. 2024 May 06; 15(1):3636. Munson BP, Chen M, Bogosian A, Kreisberg JF, Licon K, Abagyan R, Kuenzi BM, Ideker T. PMID: 38710699; PMCID: PMC11074339.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    4. 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 May 01; 5:e55976. Makunts T, Joulfayan H, Abagyan R. PMID: 38738836; PMCID: PMC11090023.
      View in: PubMed   Mentions: 2  
    5. 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 May 01; 5:e58273. Makunts T, Joulfayan H, Abagyan R. PMID: 38738852; PMCID: PMC11090022.
      View in: PubMed   Mentions:
    6. Co-occurring infections in cancer patients treated with checkpoint inhibitors significantly increase the risk of immune related adverse events. medRxiv. 2024 Feb 15. Makunts T, Grabska S, Grabski H, Abagyan R. PMID: 38405974; PMCID: PMC10889010.
      View in: PubMed   Mentions:
    7. Anti-TNF-α therapy induced psoriasis in rheumatoid arthritis patients according to FDA postmarketing surveillance data. Sci Rep. 2023 06 27; 13(1):10448. Joulfayan H, Makunts T, Abagyan R. PMID: 37369753; PMCID: PMC10300095.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    8. Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. Cell Genom. 2023 Jul 12; 3(7):100339. DeForest N, Kavitha B, Hu S, Isaac R, Krohn L, Wang M, Du X, De Arruda Saldanha C, Gylys J, Merli E, Abagyan R, Najmi L, Mohan V, Alnylam Human Genetics, AMP-T2D Consortium, Flannick J, Peloso GM, Gordts PLSM, Heinz S, Deaton AM, Khera AV, Olefsky J, Radha V, Majithia AR. PMID: 37492105; PMCID: PMC10363808.
      View in: PubMed   Mentions: 7     Fields:    
    9. High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds. PLoS One. 2023; 18(5):e0280232. Sauvey C, Meewan I, Ehrenkaufer G, Blevitt J, Jackson P, Abagyan R. PMID: 37159460; PMCID: PMC10168566.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    10. Discovery of Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L. Pharmaceuticals (Basel). 2022 Jun 13; 15(6). Meewan I, Kattoula J, Kattoula JY, Skinner D, Fajtová P, Giardini MA, Woodworth B, McKerrow JH, Lage de Siqueira-Neto J, O'Donoghue AJ, Abagyan R. PMID: 35745663; PMCID: PMC9230533.
      View in: PubMed   Mentions: 6  
    11. Control of Unsaturation in De Novo Fatty Acid Biosynthesis by FabA. Biochemistry. 2022 04 05; 61(7):608-615. Bartholow TG, Sztain T, Young MA, Lee DJ, Davis TD, Abagyan R, Burkart MD. PMID: 35255690; PMCID: PMC9769579.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    12. Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics. PLoS Comput Biol. 2022 02; 18(2):e1009903. Rosenthal SB, Wang H, Shi D, Liu C, Abagyan R, McEvoy LK, Chen CH. PMID: 35213535; PMCID: PMC8906581.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    13. Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events. PLoS One. 2022; 17(2):e0263402. Makunts T, Burkhart K, Abagyan R, Lee P. PMID: 35143542; PMCID: PMC8830697.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    14. Do Proton-Pump Inhibitors Cause CKD and Progression of CKD?: PRO. Kidney360. 2022 07 28; 3(7):1134-1136. Awdishu L, Abagyan R. PMID: 35919519; PMCID: PMC9337907.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    15. Common osteoporosis drug associated with increased rates of depression and anxiety. Sci Rep. 2021 12 14; 11(1):23956. Keshishi D, Makunts T, Abagyan R. PMID: 34907232; PMCID: PMC8671447.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    16. Molecular Properties of Drugs Handled by Kidney OATs and Liver OATPs Revealed by Chemoinformatics and Machine Learning: Implications for Kidney and Liver Disease. Pharmaceutics. 2021 Oct 18; 13(10). Nigam AK, Ojha AA, Li JG, Shi D, Bhatnagar V, Nigam KB, Abagyan R, Nigam SK. PMID: 34684013; PMCID: PMC8538396.
      View in: PubMed   Mentions: 9  
    17. Protein-protein interaction based substrate control in the E. coli octanoic acid transferase, LipB. RSC Chem Biol. 2021 Oct 07; 2(5):1466-1473. Bartholow TG, Sztain T, Young MA, Davis TD, Abagyan R, Burkart MD. PMID: 34704050; PMCID: PMC8495967.
      View in: PubMed   Mentions: 3  
    18. Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis. Commun Biol. 2021 03 16; 4(1):340. Bartholow TG, Sztain T, Patel A, Lee DJ, Young MA, Abagyan R, Burkart MD. PMID: 33727677; PMCID: PMC7966745.
      View in: PubMed   Mentions: 13  Translation:Cells
    19. Antineoplastic kinase inhibitors: A new class of potent anti-amoebic compounds. PLoS Negl Trop Dis. 2021 02; 15(2):e0008425. Sauvey C, Ehrenkaufer G, Shi D, Debnath A, Abagyan R. PMID: 33556060; PMCID: PMC7895358.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    20. Mtor inhibitors associated with higher cardiovascular adverse events-A large population database analysis. Clin Transplant. 2021 04; 35(4):e14228. Nguyen VN, Abagyan R, Tsunoda SM. PMID: 33476406.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    21. Differential activities of maize plant elicitor peptides as mediators of immune signaling and herbivore resistance. Plant J. 2020 12; 104(6):1582-1602. Poretsky E, Dressano K, Weckwerth P, Ruiz M, Char SN, Shi D, Abagyan R, Yang B, Huffaker A. PMID: 33058410.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    22. A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Proc Natl Acad Sci U S A. 2020 12 08; 117(49):31510-31518. Steinbrenner AD, Muñoz-Amatriaín M, Chaparro AF, Aguilar-Venegas JM, Lo S, Okuda S, Glauser G, Dongiovanni J, Shi D, Hall M, Crubaugh D, Holton N, Zipfel C, Abagyan R, Turlings TCJ, Close TJ, Huffaker A, Schmelz EA. PMID: 33229576; PMCID: PMC7733821.
      View in: PubMed   Mentions: 28     Fields:    Translation:Animals
    23. How can proton pump inhibitors damage central and peripheral nervous systems? Neural Regen Res. 2020 Nov; 15(11):2041-2042. Makunts T, Abagyan R. PMID: 32394957; PMCID: PMC7716020.
      View in: PubMed   Mentions: 2  
    24. HMG-CoA Reductase Inhibitors as Drug Leads against Naegleria fowleri. ACS Chem Neurosci. 2020 10 07; 11(19):3089-3096. Hahn HJ, Abagyan R, Podust LM, Roy S, Ali IKM, Debnath A. PMID: 32881478; PMCID: PMC7544672.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimals
    25. Postmarketing safety surveillance data reveals antidepressant effects of botulinum toxin across various indications and injection sites. Sci Rep. 2020 07 30; 10(1):12851. Makunts T, Wollmer MA, Abagyan R. PMID: 32732918; PMCID: PMC7393507.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    26. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol. 2020 04; 18(4):e3000656. Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM, Kufareva I. PMID: 32271748; PMCID: PMC7173943.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    27. Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs. Int J Mol Sci. 2020 Mar 05; 21(5). Engelhart DC, Granados JC, Shi D, Saier Jr MH, Baker ME, Abagyan R, Nigam SK. PMID: 32150922; PMCID: PMC7084758.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    28. Druggable exosites of the human kino-pocketome. J Comput Aided Mol Des. 2020 03; 34(3):219-230. Nicola G, Kufareva I, Ilatovskiy AV, Abagyan R. PMID: 31925639; PMCID: PMC7082431.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    29. Unique metabolite preferences of the drug transporters OAT1 and OAT3 analyzed by machine learning. J Biol Chem. 2020 02 14; 295(7):1829-1842. Nigam AK, Li JG, Lall K, Shi D, Bush KT, Bhatnagar V, Abagyan R, Nigam SK. PMID: 31896576; PMCID: PMC7029110.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    30. Proton-pump inhibitor use is associated with a broad spectrum of neurological adverse events including impaired hearing, vision, and memory. Sci Rep. 2019 11 21; 9(1):17280. Makunts T, Alpatty S, Lee KC, Atayee RS, Abagyan R. PMID: 31754136; PMCID: PMC6872761.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    31. Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors. Sci Rep. 2019 11 04; 9(1):15893. Kufareva I, Bestgen B, Brear P, Prudent R, Laudet B, Moucadel V, Ettaoussi M, Sautel CF, Krimm I, Engel M, Filhol O, Borgne ML, Lomberget T, Cochet C, Abagyan R. PMID: 31685885; PMCID: PMC6828666.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    32. Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery. Parasit Vectors. 2019 Oct 22; 12(1):493. Maccesi M, Aguiar PHN, Pasche V, Padilla M, Suzuki BM, Montefusco S, Abagyan R, Keiser J, Mourão MM, Caffrey CR. PMID: 31640761; PMCID: PMC6805474.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    33. Identification of Four Amoebicidal Nontoxic Compounds by a Molecular Docking Screen of Naegleria fowleri Sterol Δ8-Δ7-Isomerase and Phenotypic Assays. ACS Infect Dis. 2019 12 13; 5(12):2029-2038. Shi D, Chahal KK, Oto P, Nothias LF, Debnath A, McKerrow JH, Podust LM, Abagyan R. PMID: 31583882; PMCID: PMC7085920.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    34. Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant. ACS Omega. 2019 Oct 15; 4(16):16999-17008. Meewan I, Zhang X, Roy S, Ballatore C, O'Donoghue AJ, Schooley RT, Abagyan R. PMID: 31646247; PMCID: PMC6796237.
      View in: PubMed   Mentions: 10  
    35. Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma. PLoS One. 2019; 14(9):e0214901. Chahal KK, Li J, Kufareva I, Parle M, Durden DL, Wechsler-Reya RJ, Chen CC, Abagyan R. PMID: 31539380; PMCID: PMC6754133.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    36. Retrospective analysis reveals significant association of hypoglycemia with tramadol and methadone in contrast to other opioids. Sci Rep. 2019 08 28; 9(1):12490. Makunts T, U A, Atayee RS, Abagyan R. PMID: 31462666; PMCID: PMC6713717.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    37. Extended Multitarget Pharmacology of Anticancer Drugs. J Chem Inf Model. 2019 06 24; 59(6):3006-3017. Shi D, Khan F, Abagyan R. PMID: 31025863; PMCID: PMC7100364.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    38. Analysis of postmarketing safety data for proton-pump inhibitors reveals increased propensity for renal injury, electrolyte abnormalities, and nephrolithiasis. Sci Rep. 2019 02 19; 9(1):2282. Makunts T, Cohen IV, Awdishu L, Abagyan R. PMID: 30783195; PMCID: PMC6381091.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    39. Molecular Basis of Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor. Mol Pharmacol. 2019 03; 95(3):245-259. Desai AJ, Mechin I, Nagarajan K, Valant C, Wootten D, Lam PCH, Orry A, Abagyan R, Nair A, Sexton PM, Christopoulos A, Miller LJ. PMID: 30591538.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    40. Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain. PLoS One. 2018; 13(4):e0195521. Makunts T, Cohen IV, Lee KC, Abagyan R. PMID: 29668764; PMCID: PMC5905979.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    41. Revisiting Antipsychotic Drug Actions Through Gene Networks Associated With Schizophrenia. Am J Psychiatry. 2018 07 01; 175(7):674-682. Kauppi K, Rosenthal SB, Lo MT, Sanyal N, Jiang M, Abagyan R, McEvoy LK, Andreassen OA, Chen CH. PMID: 29495895; PMCID: PMC6028303.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    42. CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM). PLoS Negl Trop Dis. 2017 12; 11(12):e0006104. Debnath A, Calvet CM, Jennings G, Zhou W, Aksenov A, Luth MR, Abagyan R, Nes WD, McKerrow JH, Podust LM. PMID: 29284029; PMCID: PMC5746216.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    43. Publisher Correction: Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications. Sci Rep. 2017 12 05; 7(1):17268. Cohen IV, Makunts T, Atayee R, Abagyan R. PMID: 29208902; PMCID: PMC5717077.
      View in: PubMed   Mentions: 1     Fields:    
    44. Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor. Nucleic Acids Res. 2017 Sep 06; 45(15):8835-8843. Shi D, Svetlov D, Abagyan R, Artsimovitch I. PMID: 28605514; PMCID: PMC5587751.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    45. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity. 2017 06 20; 46(6):1005-1017.e5. Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM. PMID: 28636951; PMCID: PMC5572563.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansAnimalsCells
    46. Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications. Sci Rep. 2017 05 03; 7(1):1450. Cohen IV, Makunts T, Atayee R, Abagyan R. PMID: 28469132; PMCID: PMC5431207.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    47. Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 2017 01 18; 8:14135. Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. PMID: 28098154; PMCID: PMC5253664.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    48. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature. 2016 12 15; 540(7633):458-461. Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, Handel TM. PMID: 27926736; PMCID: PMC5159191.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansCells
    49. Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach. J Pharmacol Exp Ther. 2016 10; 359(1):215-29. Liu HC, Goldenberg A, Chen Y, Lun C, Wu W, Bush KT, Balac N, Rodriguez P, Abagyan R, Nigam SK. PMID: 27488918; PMCID: PMC5034704.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    50. Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada. PLoS One. 2015; 10(12):e0144337. Ali TB, Schleret TR, Reilly BM, Chen WY, Abagyan R. PMID: 26642212; PMCID: PMC4671709.
      View in: PubMed   Mentions: 48     Fields:    Translation:Humans
    51. Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors. Drug Metab Dispos. 2015 Dec; 43(12):1855-63. Wu W, Bush KT, Liu HC, Zhu C, Abagyan R, Nigam SK. PMID: 26358290; PMCID: PMC4658493.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    52. P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Mol Cell. 2015 Sep 17; 59(6):931-40. Skowronska-Krawczyk D, Zhao L, Zhu J, Weinreb RN, Cao G, Luo J, Flagg K, Patel S, Wen C, Krupa M, Luo H, Ouyang H, Lin D, Wang W, Li G, Xu Y, Li O, Chung C, Yeh E, Jafari M, Ai M, Zhong Z, Shi W, Zheng L, Krawczyk M, Chen D, Shi C, Zin C, Zhu J, Mellon PL, Gao W, Abagyan R, Zhang L, Sun X, Zhong S, Zhuo Y, Rosenfeld MG, Liu Y, Zhang K. PMID: 26365380; PMCID: PMC4648709.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    53. Lanosterol reverses protein aggregation in cataracts. Nature. 2015 Jul 30; 523(7562):607-11. Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Jefferson J, Perry P, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K. PMID: 26200341.
      View in: PubMed   Mentions: 150     Fields:    Translation:HumansAnimalsCells
    54. Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling. Dev Cell. 2015 Apr 20; 33(2):189-203. Lo IC, Gupta V, Midde KK, Taupin V, Lopez-Sanchez I, Kufareva I, Abagyan R, Randazzo PA, Farquhar MG, Ghosh P. PMID: 25865347; PMCID: PMC4415880.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    55. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science. 2015 Mar 06; 347(6226):1117-22. Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM. PMID: 25612609; PMCID: PMC4362693.
      View in: PubMed   Mentions: 187     Fields:    Translation:HumansCells
    56. Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol. 2015; 1335:295-311. Kufareva I, Handel TM, Abagyan R. PMID: 26260608; PMCID: PMC4551442.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    57. Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):E5363-72. Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM. PMID: 25468967; PMCID: PMC4273337.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    58. Development of a highly selective allosteric antagonist radioligand for the type 1 cholecystokinin receptor and elucidation of its molecular basis of binding. Mol Pharmacol. 2015 Jan; 87(1):130-40. Dong M, Vattelana AM, Lam PC, Orry AJ, Abagyan R, Christopoulos A, Sexton PM, Haines DR, Miller LJ. PMID: 25319540; PMCID: PMC4279081.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    59. Discovery of novel membrane binding structures and functions. Biochem Cell Biol. 2014 Dec; 92(6):555-63. Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M. PMID: 25394204; PMCID: PMC4267288.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    60. Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Mol Biol Cell. 2014 Nov 05; 25(22):3654-71. Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P. PMID: 25187647; PMCID: PMC4230624.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    61. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. 2014 Aug 05; 22(8):1120-1139. Kufareva I, Katritch V, Participants of GPCR Dock 2013, Stevens RC, Abagyan R. PMID: 25066135; PMCID: PMC4126895.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansCells
    62. In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. Toxicol Sci. 2014 Sep; 141(1):188-97. McRobb FM, Kufareva I, Abagyan R. PMID: 24928891; PMCID: PMC4271121.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    63. A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 2014; 9(1):e81454. Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM. PMID: 24489642; PMCID: PMC3904831.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    64. In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol. 2014; 48(3):1964-72. McRobb FM, Sahagún V, Kufareva I, Abagyan R. PMID: 24392850; PMCID: PMC3951377.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    65. PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):717-23. Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R. PMID: 24406170; PMCID: PMC3975830.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    66. Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. Future Med Chem. 2014; 6(16):1741-55. Chen YC, Totrov M, Abagyan R. PMID: 25407367; PMCID: PMC4285145.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    67. The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers. Mol Pharmacol. 2014 Feb; 85(2):301-9. Kennedy DP, McRobb FM, Leonhardt SA, Purdy M, Figler H, Marshall MA, Chordia M, Figler R, Linden J, Abagyan R, Yeager M. PMID: 24217444; PMCID: PMC3913357.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    68. Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol. 2013 Dec; 84(6):794-807. Lane JR, Chubukov P, Liu W, Canals M, Cherezov V, Abagyan R, Stevens RC, Katritch V. PMID: 24021214; PMCID: PMC3834142.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    69. Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. Int J Quantum Chem. 2013 Jun 15; 113(12):1669-1675. Ilatovskiy AV, Abagyan R, Kufareva I. PMID: 25414519; PMCID: PMC4235788.
      View in: PubMed   Mentions: 7  
    70. A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods Mol Biol. 2013; 1013:93-127. Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM. PMID: 23625495; PMCID: PMC4091634.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    71. ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model. 2012 Oct 22; 52(10):2705-14. Rueda M, Totrov M, Abagyan R. PMID: 22947092; PMCID: PMC3478405.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    72. Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des. 2012 Jun; 26(6):675-86. Neves MA, Totrov M, Abagyan R. PMID: 22569591; PMCID: PMC3398187.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansCells
    73. Unusual arginine formations in protein function and assembly: rings, strings, and stacks. J Phys Chem B. 2012 Jun 14; 116(23):7006-13. Neves MA, Yeager M, Abagyan R. PMID: 22497303; PMCID: PMC3613333.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    74. Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem. 2012; 12(17):1869-82. Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R. PMID: 23116466; PMCID: PMC4085113.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    75. Methods of protein structure comparison. Methods Mol Biol. 2012; 857:231-57. Kufareva I, Abagyan R. PMID: 22323224; PMCID: PMC4321859.
      View in: PubMed   Mentions: 170     Fields:    Translation:Cells
    76. Ligand-guided receptor optimization. Methods Mol Biol. 2012; 857:189-205. Katritch V, Rueda M, Abagyan R. PMID: 22323222.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    77. Computational chemistry in 25 years. J Comput Aided Mol Des. 2012 Jan; 26(1):9-10. Abagyan R. PMID: 22160588.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    78. Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 2012 Jan; 40(Database issue):D535-40. Kufareva I, Ilatovskiy AV, Abagyan R. PMID: 22080553; PMCID: PMC3245087.
      View in: PubMed   Mentions: 69     Fields:    Translation:Cells
    79. Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal. 2011 Sep 27; 4(192):ra64. Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P. PMID: 21954290; PMCID: PMC4226136.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    80. GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci. 2011 Nov; 32(11):637-43. Katritch V, Abagyan R. PMID: 21903279; PMCID: PMC3200445.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    81. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. 2011 Aug 10; 19(8):1108-26. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R, GPCR Dock 2010 participants. PMID: 21827947; PMCID: PMC3154726.
      View in: PubMed   Mentions: 115     Fields:    Translation:HumansCells
    82. SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. Bioinformatics. 2010 Nov 01; 26(21):2784-5. Rueda M, Katritch V, Raush E, Abagyan R. PMID: 20871105; PMCID: PMC2981495.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    83. Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology. 2011 Jan; 60(1):108-15. Katritch V, Kufareva I, Abagyan R. PMID: 20637786; PMCID: PMC2980563.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    84. Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem. 2010 Feb 25; 53(4):1799-809. Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R. PMID: 20095623; PMCID: PMC2826142.
      View in: PubMed   Mentions: 100     Fields:    Translation:HumansAnimalsCells
    85. 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A. 2007 Nov 20; 104(47):18619-24. Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva I, Abagyan R, Broide DH, Lee J, Raz E. PMID: 18003900; PMCID: PMC2141826.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansAnimalsCells
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