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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 selected 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. Structure based design, synthesis and identification of novel covalent reversible dual TLR2/TLR9 small molecule antagonists. Bioorg Med Chem Lett. 2025 Aug 15; 124:130259. Natala SR, Habas A, Stocking EM, Orry A, Abagyan R, Makale MT, Wrasidlo W. PMID: 40294721.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. Identifying Allosteric Small-Molecule Binding Sites of Inactive NS2B-NS3 Proteases of Pathogenic Flaviviridae. Viruses. 2024 12 24; 17(1). Grabski H, Grabska S, Abagyan R. PMID: 39861795; PMCID: PMC11769402.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. Correction: Cytomembrane-mimicking nanocarriers with a scaffold consisting of a CD44-targeted endogenous component for effective asparaginase supramolecule delivery. Nanoscale. 2024 Dec 05; 16(47):22048-22049. Huang Y, Gu J, Yan Z, Hu X, He D, Zhang Y, Li Y, Zhong C, Yang J, Shi D, Abagyan R, Tan Q, Zhang J. PMID: 39574406.
      View in: PubMed   Mentions:    Fields:    
    4. 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:
    5. 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:
    6. 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: 21     Fields:    Translation:HumansCells
    7. 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: 5  
    8. 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:
    9. Efficient Generation of Conformer Ensembles Using Internal Coordinates and a Generative Directional Graph Convolution Neural Network. J Chem Theory Comput. 2024 May 14; 20(9):4054-4063. Raush E, Abagyan R, Totrov M. PMID: 38669307.
      View in: PubMed   Mentions: 3     Fields:    
    10. 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:
    11. Software and Databases for Protein-Protein Docking. Methods Mol Biol. 2024; 2780:129-138. Jaronczyk M, Abagyan R, Totrov M. PMID: 38987467.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    12. Thyroid hyperplasia and neoplasm adverse events associated with GLP-1 receptor agonists in FDA Adverse Event Reporting System. medRxiv. 2023 Nov 24. Makunts T, Joulfayan H, Abagyan R. PMID: 38045343; PMCID: PMC10690345.
      View in: PubMed   Mentions:
    13. 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: 3     Fields:    Translation:Humans
    14. 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: 11     Fields:    
    15. Concomitant medications associated with ischemic, hypertensive, and arrhythmic events in MDMA users in FDA adverse event reporting system. Front Psychiatry. 2023; 14:1149766. Makunts T, Dahill D, Jerome L, de Boer A, Abagyan R. PMID: 37275981; PMCID: PMC10233020.
      View in: PubMed   Mentions: 2  
    16. 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
    17. Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in "Super-Open" Conformation. Viruses. 2023 04 30; 15(5). Meewan I, Shiryaev SA, Kattoula J, Huang CT, Lin V, Chuang CH, Terskikh AV, Abagyan R. PMID: 37243192; PMCID: PMC10224173.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    18. Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. J Chem Inf Model. 2022 Dec 12; 62(23):5896-5906. Raush E, Abagyan R, Totrov M. PMID: 36456533.
      View in: PubMed   Mentions:    Fields:    
    19. 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: 7  
    20. 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: 2     Fields:    Translation:Cells
    21. 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: 13     Fields:    Translation:AnimalsCells
    22. 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: 5     Fields:    Translation:Humans
    23. Reported Cases of Serotonin Syndrome in MDMA Users in FAERS Database. Front Psychiatry. 2021; 12:824288. Makunts T, Jerome L, Abagyan R, de Boer A. PMID: 35140642; PMCID: PMC8820588.
      View in: PubMed   Mentions: 7  
    24. 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
    25. Postmarketing safety surveillance data reveals protective effects of botulinum toxin injections against incident anxiety. Sci Rep. 2021 12 21; 11(1):24173. Wollmer MA, Makunts T, Krüger THC, Abagyan R. PMID: 34934096; PMCID: PMC8692576.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    26. ARN25068, a versatile starting point towards triple GSK-3β/FYN/DYRK1A inhibitors to tackle tau-related neurological disorders. Eur J Med Chem. 2022 Feb 05; 229:114054. Demuro S, Sauvey C, Tripathi SK, Di Martino RMC, Shi D, Ortega JA, Russo D, Balboni B, Giabbai B, Storici P, Girotto S, Abagyan R, Cavalli A. PMID: 34959172; PMCID: PMC9704499.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    27. 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: 16     Fields:    Translation:Humans
    28. 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  
    29. Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Comput Biol. 2021 09; 17(9):e1009302. Xiong Z, Jeon M, Allaway RJ, Kang J, Park D, Lee J, Jeon H, Ko M, Jiang H, Zheng M, Tan AC, Guo X, Multi-Targeting Drug DREAM Challenge Community, Dang KK, Tropsha A, Hecht C, Das TK, Carlson HA, Abagyan R, Guinney J, Schlessinger A, Cagan R. PMID: 34520464; PMCID: PMC8483411.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    30. Myocarditis occurrence with cancer immunotherapy across indications in clinical trial and post-marketing data. Sci Rep. 2021 08 30; 11(1):17324. Makunts T, Saunders IM, Cohen IV, Li M, Moumedjian T, Issa MA, Burkhart K, Lee P, Patel SP, Abagyan R. PMID: 34462476; PMCID: PMC8405813.
      View in: PubMed   Mentions: 30     Fields:    Translation:Humans
    31. 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: 4  
    32. Retraction Note: Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2021 Apr; 17(4):501. Ngo T, Ilatovskiy AV, Stewart AG, Coleman JLJ, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ. PMID: 33649604; PMCID: PMC7990710.
      View in: PubMed   Mentions: 1     Fields:    
    33. Concomitant drugs associated with increased mortality for MDMA users reported in a drug safety surveillance database. Sci Rep. 2021 03 16; 11(1):5997. Cohen IV, Makunts T, Abagyan R, Thomas K. PMID: 33727616; PMCID: PMC7966744.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansPHPublic Health
    34. 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: 15  Translation:Cells
    35. Structure based design and synthesis of novel Toll-like Receptor 2 (TLR 2) lipid antagonists. Bioorg Med Chem Lett. 2021 05 15; 40:127861. Natala SR, Habas A, Stocking EM, Orry A, Price DL, Gill MB, Bonhaus DW, Abagyan R, Wrasidlo W. PMID: 33636302.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    36. 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
    37. 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: 5     Fields:    Translation:Humans
    38. 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: 10     Fields:    Translation:Animals
    39. 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: 45     Fields:    Translation:Animals
    40. Cardiac adverse events associated with chloroquine and hydroxychloroquine exposure in 20 years of drug safety surveillance reports. Sci Rep. 2020 11 05; 10(1):19199. Cohen IV, Makunts T, Moumedjian T, Issa MA, Abagyan R. PMID: 33154498; PMCID: PMC7644696.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansPHPublic Health
    41. 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: 4  
    42. Biomimetic microbioreactor-supramolecular nanovesicles improve enzyme therapy of hepatic cancer. Nanomedicine. 2021 01; 31:102311. He X, Feng J, Yan S, Zhang Y, Zhong C, Liu Y, Shi D, Abagyan R, Xiang T, Zhang J. PMID: 33011392.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    43. 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: 12     Fields:    Translation:HumansAnimals
    44. Synthesis, Optimization, Antifungal Activity, Selectivity, and CYP51 Binding of New 2-Aryl-3-azolyl-1-indolyl-propan-2-ols. Pharmaceuticals (Basel). 2020 Aug 08; 13(8). Lebouvier N, Pagniez F, Na YM, Shi D, Pinson P, Marchivie M, Guillon J, Hakki T, Bernhardt R, Yee SW, Simons C, Lézé MP, Hartmann RW, Mularoni A, Le Baut G, Krimm I, Abagyan R, Le Pape P, Le Borgne M. PMID: 32784450; PMCID: PMC7464559.
      View in: PubMed   Mentions: 4  
    45. 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
    46. Biomimetic polysaccharide-cloaked lipidic nanovesicles/microassemblies for improving the enzymatic activity and prolonging the action time for hyperuricemia treatment. Nanoscale. 2020 Jul 23; 12(28):15222-15235. Yang L, Zhang Y, Xie J, Zhong C, He D, Wang T, Li K, Li Y, Shi D, Abagyan R, Yang L, Zhang J. PMID: 32639489.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    47. Biomimetic Membrane-Structured Nanovesicles Carrying a Supramolecular Enzyme to Cure Lung Cancer. ACS Appl Mater Interfaces. 2020 Jul 15; 12(28):31112-31123. Gu J, Huang Y, Yan Z, He D, Zhang Y, Xu J, Li Y, Xie X, Xie J, Shi D, Abagyan R, Zhang J, Tan Q. PMID: 32544316.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    48. Cytomembrane-mimicking nanocarriers with a scaffold consisting of a CD44-targeted endogenous component for effective asparaginase supramolecule delivery. Nanoscale. 2020 Jun 11; 12(22):12083-12097. Huang Y, Gu J, Yan Z, Hu X, He D, Zhang Y, Li Y, Zhong C, Yang J, Shi D, Abagyan R, Tan Q, Zhang J. PMID: 32478361.
      View in: PubMed   Mentions: 3     Fields:    
    49. 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: 21     Fields:    Translation:HumansAnimalsCells
    50. 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: 37     Fields:    Translation:HumansAnimalsCells
    51. Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins. Physiol Plant. 2020 May; 169(1):99-109. Graña E, Díaz-Tielas C, Sánchez-Moreiras AM, Reigosa MJ, Celeiro M, Abagyan R, Teijeira M, Duke MV, Clerk T, Pan Z, Duke SO. PMID: 31828797.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    52. Recommendations for Improving Methods and Models for Aquatic Hazard Assessment of Ionizable Organic Chemicals. Environ Toxicol Chem. 2020 02; 39(2):269-286. Escher BI, Abagyan R, Embry M, Klüver N, Redman AD, Zarfl C, Parkerton TF. PMID: 31569266.
      View in: PubMed   Mentions: 15     Fields:    Translation:Animals
    53. 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
    54. 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: 29     Fields:    Translation:HumansAnimalsCells
    55. 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: 34     Fields:    Translation:Humans
    56. 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: 7     Fields:    Translation:HumansCells
    57. 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: 17     Fields:    Translation:Animals
    58. 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
    59. Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. J Comput Aided Mol Des. 2019 12; 33(12):1057-1069. Lam PC, Abagyan R, Totrov M. PMID: 31598897.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    60. 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: 17  
    61. 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: 3     Fields:    Translation:HumansAnimalsCells
    62. 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
    63. Population Scale Retrospective Analysis Reveals Potential Risk of Cholestasis in Pregnant Women Taking Omeprazole, Lansoprazole, and Amoxicillin. Interdiscip Sci. 2019 Jun; 11(2):273-281. Zhang Y, Shi D, Abagyan R, Dai W, Dong M. PMID: 31106388; PMCID: PMC7172024.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    64. 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: 11     Fields:    Translation:Cells
    65. 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: 31     Fields:    Translation:Humans
    66. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. J Med Chem. 2019 02 28; 62(4):1803-1816. Bestgen B, Krimm I, Kufareva I, Kamal AAM, Seetoh WG, Abell C, Hartmann RW, Abagyan R, Cochet C, Le Borgne M, Engel M, Lomberget T. PMID: 30689953; PMCID: PMC7667462.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
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    68. 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.
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    69. In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase. Mol Microbiol. 2018 10; 110(1):128-142. Svetlov D, Shi D, Twentyman J, Nedialkov Y, Rosen DA, Abagyan R, Artsimovitch I. PMID: 30069925; PMCID: PMC6595482.
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    70. Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells. ACS Omega. 2018 Sep 30; 3(9):12019-12025. Chahal KK, Parle M, Abagyan R. PMID: 31459282; PMCID: PMC6645496.
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    73. Hedgehog pathway and smoothened inhibitors in cancer therapies. Anticancer Drugs. 2018 06; 29(5):387-401. Chahal KK, Parle M, Abagyan R. PMID: 29537987.
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    74. 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.
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    77. 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.
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    79. 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.
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    85. 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.
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    86. A Thiazole Orange Derivative Targeting the Bacterial Protein FtsZ Shows Potent Antibacterial Activity. Front Microbiol. 2017; 8:855. Sun N, Lu YJ, Chan FY, Du RL, Zheng YY, Zhang K, So LY, Abagyan R, Zhuo C, Leung YC, Wong KY. PMID: 28553278; PMCID: PMC5426085.
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    93. Correction to Environmental Photochemistry of Altrenogest: Photoisomerization to a Bioactive Product with Increased Environmental Persistence via Reversible Photohydration. Environ Sci Technol. 2016 09 20; 50(18):10292. Wammer KH, Anderson KC, Erickson PR, Kliegman S, Moffatt ME, Berg SM, Heitzman JA, Pflug NC, McNeill K, Martinovic-Weigelt D, Abagyan R, Cwiertny DM, Kolodziej EP. PMID: 27604407.
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    98. Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters. J Chem Theory Comput. 2016 Jul 12; 12(7):3236-49. Pallara C, Rueda M, Abagyan R, Fernández-Recio J. PMID: 27294484.
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    99. Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor. Cell Res. 2016 05; 26(5):574-92. Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A. PMID: 27002221; PMCID: PMC4856764.
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    101. X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action. J Struct Biol. 2016 May; 194(2):180-90. Parsonage D, Sheng F, Hirata K, Debnath A, McKerrow JH, Reed SL, Abagyan R, Poole LB, Podust LM. PMID: 26876147; PMCID: PMC5003402.
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    102. An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels. Nat Commun. 2016 Jan 12; 7:8770. Bennett BC, Purdy MD, Baker KA, Acharya C, McIntire WE, Stevens RC, Zhang Q, Harris AL, Abagyan R, Yeager M. PMID: 26753910; PMCID: PMC4730032.
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    103. Use of Cysteine Trapping to Map Spatial Approximations between Residues Contributing to the Helix N-capping Motif of Secretin and Distinct Residues within Each of the Extracellular Loops of Its Receptor. J Biol Chem. 2016 Mar 04; 291(10):5172-84. Dong M, Lam PC, Orry A, Sexton PM, Christopoulos A, Abagyan R, Miller LJ. PMID: 26740626; PMCID: PMC4777851.
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    104. Molecular Mechanism of Action of Triazolobenzodiazepinone Agonists of the Type 1 Cholecystokinin Receptor. Possible Cooperativity across the Receptor Homodimeric Complex. J Med Chem. 2015 Dec 24; 58(24):9562-77. Desai AJ, Lam PC, Orry A, Abagyan R, Christopoulos A, Sexton PM, Miller LJ. PMID: 26654202; PMCID: PMC4790425.
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    105. 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.
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    110. Corrigendum: Lanosterol reverses protein aggregation in cataracts. Nature. 2015 Oct 22; 526(7574):595. 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, Perry JJ, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K. PMID: 26308894.
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    114. FOCUS--Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. J Chem Inf Model. 2015 Apr 27; 55(4):896-908. Stiefl N, Gedeck P, Chin D, Hunt P, Lindvall M, Spiegel K, Springer C, Biller S, Buenemann C, Kanazawa T, Kato M, Lewis R, Martin E, Polyakov V, Tommasi R, van Drie J, Vash B, Whitehead L, Xu Y, Abagyan R, Raush E, Totrov M. PMID: 25816021.
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    126. Sequence-conserved and antibody-accessible sites in the V1V2 domain of HIV-1 gp120 envelope protein. AIDS Res Hum Retroviruses. 2014 Sep; 30(9):927-31. Shmelkov E, Grigoryan A, Krachmarov C, Abagyan R, Cardozo T. PMID: 25051095; PMCID: PMC4151074.
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    128. 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.
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    129. Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity. PLoS One. 2014; 9(5):e97514. Sun N, Chan FY, Lu YJ, Neves MA, Lui HK, Wang Y, Chow KY, Chan KF, Yan SC, Leung YC, Abagyan R, Chan TH, Wong KY. PMID: 24824618; PMCID: PMC4019636.
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    130. Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model. 2014 Mar 24; 54(3):933-43. Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ. PMID: 24521202; PMCID: PMC3982395.
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    131. 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.
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    132. 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.
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    133. 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.
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    134. 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.
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    135. Computational evidence for the reactivation process of human acetylcholinesterase inhibited by carbamates. Comb Chem High Throughput Screen. 2014; 17(6):554-64. Matos KS, da Cunha EF, Abagyan R, Ramalho TC. PMID: 24344993.
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    136. BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC Struct Biol. 2013 Dec 13; 13:32. Rueda M, Orozco M, Totrov M, Abagyan R. PMID: 24330655; PMCID: PMC3924234.
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    137. 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.
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    138. Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor Biol Med Model. 2013 Sep 14; 10:56. Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW. PMID: 24034446; PMCID: PMC3848485.
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    139. 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.
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    140. Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening. J Chem Inf Model. 2013 Aug 26; 53(8):2131-40. Chan FY, Sun N, Neves MA, Lam PC, Chung WH, Wong LK, Chow HY, Ma DL, Chan PH, Leung YC, Chan TH, Abagyan R, Wong KY. PMID: 23848971.
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    141. 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.
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    142. Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. J Biol Chem. 2013 Jul 19; 288(29):21082-21095. Harikumar KG, Cawston EE, Lam PCH, Patil A, Orry A, Henke BR, Abagyan R, Christopoulos A, Sexton PM, Miller LJ. PMID: 23754289; PMCID: PMC3774375.
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    143. Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell. 2013 May 28; 25(4):364-73. Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg J. PMID: 23664863; PMCID: PMC4129370.
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    144. Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors. Chem Biol Drug Des. 2013 Jun; 81(6):695-706. Gabrielsen M, Wolosewicz K, Zawadzka A, Kossakowski J, Nowak G, Wolak M, Stachowicz K, Siwek A, Ravna AW, Kufareva I, Kozerski L, Bednarek E, Sitkowski J, Bocian W, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. PMID: 23574807; PMCID: PMC3665732.
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    145. Predicting p Ka values from EEM atomic charges. J Cheminform. 2013 Apr 10; 5(1):18. Vareková RS, Geidl S, Ionescu CM, Skrehota O, Bouchal T, Sehnal D, Abagyan R, Koca J. PMID: 23574978; PMCID: PMC3663834.
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    146. Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One. 2013; 8(2):e56150. Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan R, Mensa-Wilmot K. PMID: 23437089; PMCID: PMC3577790.
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    147. 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.
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    148. Designing Endocrine Disruption Out of the Next Generation of Chemicals. Green Chem. 2013 Jan; 15(1):181-198. Schug TT, Abagyan R, Blumberg B, Collins TJ, Crews D, DeFur PL, Dickerson SM, Edwards TM, Gore AC, Guillette LJ, Hayes T, Heindel JJ, Moores A, Patisaul HB, Tal TL, Thayer KA, Vandenberg LN, Warner J, Watson CS, Saal FS, Zoeller RT, O'Brien KP, Myers JP. PMID: 25110461; PMCID: PMC4125359.
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    149. The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov. 2013 01; 12(1):25-34. Stevens RC, Cherezov V, Katritch V, Abagyan R, Kuhn P, Rosen H, Wüthrich K. PMID: 23237917; PMCID: PMC3723354.
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    150. Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annu Rev Pharmacol Toxicol. 2013; 53:331-54. Montaner S, Kufareva I, Abagyan R, Gutkind JS. PMID: 23092247; PMCID: PMC4074518.
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    151. Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization. J Med Chem. 2012 Sep 27; 55(18):7998-8006. Wein AN, Williams BN, Liu S, Ermolinsky B, Provenzano D, Abagyan R, Orry A, Leppla SH, Peredelchuk M. PMID: 22954387; PMCID: PMC3474531.
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    152. 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.
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    153. Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB J. 2012 Dec; 26(12):5092-105. Dong M, Xu X, Ball AM, Makhoul JA, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ. PMID: 22964305; PMCID: PMC3509059.
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    154. A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl. 2012 Sep 03; 51(36):9010-4. Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DS, Ma VP, Abagyan R, Wong CY, Ma DL. PMID: 22807261.
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    155. 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.
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    156. Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds. J Chem Inf Model. 2012 May 25; 52(5):1367-75. Chan FY, Neves MA, Sun N, Tsang MW, Leung YC, Chan TH, Abagyan R, Wong KY. PMID: 22559726.
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    157. Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J Med Chem. 2012 May 10; 55(9):4297-308. Tosh DK, Phan K, Gao ZG, Gakh AA, Xu F, Deflorian F, Abagyan R, Stevens RC, Jacobson KA, Katritch V. PMID: 22486652; PMCID: PMC3479662.
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    158. 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.
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    159. Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor. J Biol Chem. 2012 May 25; 287(22):18618-35. Cawston EE, Lam PC, Harikumar KG, Dong M, Ball AM, Augustine ML, Akgün E, Portoghese PS, Orry A, Abagyan R, Sexton PM, Miller LJ. PMID: 22467877; PMCID: PMC3365725.
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    160. Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. J Med Chem. 2012 Apr 12; 55(7):3049-57. Sager G, Ørvoll EØ, Lysaa RA, Kufareva I, Abagyan R, Ravna AW. PMID: 22380603; PMCID: PMC4181661.
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    161. Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. Eur J Med Chem. 2012 Mar; 49:200-10. Jaronczyk M, Wolosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. PMID: 22309909; PMCID: PMC3365592.
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    162. Preparation and refinement of model protein-ligand complexes. Methods Mol Biol. 2012; 857:351-73. Orry AJ, Abagyan R. PMID: 22323230.
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    163. 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.
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    164. Ligand-guided receptor optimization. Methods Mol Biol. 2012; 857:189-205. Katritch V, Rueda M, Abagyan R. PMID: 22323222.
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    165. Methods of protein structure comparison. Methods Mol Biol. 2012; 857:231-57. Kufareva I, Abagyan R. PMID: 22323224; PMCID: PMC4321859.
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    166. Computational chemistry in 25 years. J Comput Aided Mol Des. 2012 Jan; 26(1):9-10. Abagyan R. PMID: 22160588.
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    167. 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.
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    168. Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. Eur J Med Chem. 2012 Jan; 47(1):24-37. Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z, Bojarski AJ, Sylte I. PMID: 22071255; PMCID: PMC3357065.
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    169. 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.
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    170. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. J Comput Aided Mol Des. 2011 Oct; 25(10):895-911. Bordner AJ, Zorman B, Abagyan R. PMID: 21904908; PMCID: PMC4175375.
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    171. 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.
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    172. 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.
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    173. Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes. J Chem Inf Model. 2011 Aug 22; 51(8):1795-806. Svobodová Vareková R, Geidl S, Ionescu CM, Skrehota O, Kudera M, Sehnal D, Bouchal T, Abagyan R, Huber HJ, Koca J. PMID: 21761919.
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    174. Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure. 2011 Jul 13; 19(7):930-44. Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley SK, Darnell RB, Patel DJ. PMID: 21742260; PMCID: PMC3134789.
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    175. Structure of the human histamine H1 receptor complex with doxepin. Nature. 2011 Jun 22; 475(7354):65-70. Shimamura T, Shiroishi M, Weyand S, Tsujimoto H, Winter G, Katritch V, Abagyan R, Cherezov V, Liu W, Han GW, Kobayashi T, Stevens RC, Iwata S. PMID: 21697825; PMCID: PMC3131495.
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    176. Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One. 2011; 6(5):e18845. Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A. PMID: 21625529; PMCID: PMC3098722.
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    177. Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem. 2011 Jul 08; 286(27):23888-99. Dong M, Lam PC, Pinon DI, Hosohata K, Orry A, Sexton PM, Abagyan R, Miller LJ. PMID: 21566140; PMCID: PMC3129170.
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    178. Interactive JIMD articles using the iSee concept: turning a new page on structural biology data. J Inherit Metab Dis. 2011 Jun; 34(3):565-7. Lee WH, Yue WW, Raush E, Totrov M, Abagyan R, Oppermann U, Marsden BD. PMID: 21509537.
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    179. Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. J Biol Chem. 2011 May 06; 286(18):15895-907. Miller LJ, Chen Q, Lam PC, Pinon DI, Sexton PM, Abagyan R, Dong M. PMID: 21454562; PMCID: PMC3091199.
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    180. Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins. 2011 Feb; 79(2):477-98. Arnautova YA, Abagyan RA, Totrov M. PMID: 21069716; PMCID: PMC3057902.
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    181. A natural product-like inhibitor of NEDD8-activating enzyme. Chem Commun (Camb). 2011 Mar 07; 47(9):2511-3. Leung CH, Chan DS, Yang H, Abagyan R, Lee SM, Zhu GY, Fong WF, Ma DL. PMID: 21240405.
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    182. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science. 2010 Nov 19; 330(6007):1066-71. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC. PMID: 20929726; PMCID: PMC3074590.
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    183. 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.
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    184. Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc. 2010 Aug 25; 132(33):11443-5. Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, Stevens RC. PMID: 20669948; PMCID: PMC2923663.
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    185. The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening. J Med Chem. 2010 Jul 22; 53(14):5267-80. Odell LR, Howan D, Gordon CP, Robertson MJ, Chau N, Mariana A, Whiting AE, Abagyan R, Daniel JA, Gorgani NN, Robinson PJ, McCluskey A. PMID: 20575553.
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    186. Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology. 2010 Sep 30; 405(2):513-23. Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S. PMID: 20663531; PMCID: PMC2942080.
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    187. 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.
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    188. Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol. 2010 May 28; 17(5):471-82. Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H, Larocca C, Saldanha SA, Abagyan R, Sun Y, Meyers DJ, Marmorstein R, Mahadevan LC, Alani RM, Cole PA. PMID: 20534345; PMCID: PMC2884008.
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    189. Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention. J Med Chem. 2010 May 27; 53(10):3899-906. Cheltsov AV, Aoyagi M, Aleshin A, Yu EC, Gilliland T, Zhai D, Bobkov AA, Reed JC, Liddington RC, Abagyan R. PMID: 20441222; PMCID: PMC2874095.
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    190. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des. 2010 May; 24(5):459-71. Park SJ, Kufareva I, Abagyan R. PMID: 20455005; PMCID: PMC2881208.
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    191. Structure-based discovery of natural-product-like TNF-α inhibitors. Angew Chem Int Ed Engl. 2010 Apr 06; 49(16):2860-4. Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL. PMID: 20235259; PMCID: PMC4162403.
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    192. Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des. 2010 Mar; 24(3):173-82. Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. PMID: 20229197; PMCID: PMC2858276.
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    193. 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.
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    194. Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment. J Biol Chem. 2010 Mar 26; 285(13):9919-9931. Dong M, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ. PMID: 20100828; PMCID: PMC2843239.
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    195. GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins. 2010 Jan; 78(1):197-211. Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R. PMID: 20063437; PMCID: PMC2805832.
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    196. Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model. 2010 Jan; 50(1):186-93. Rueda M, Bottegoni G, Abagyan R. PMID: 20000587; PMCID: PMC2811216.
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    197. A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway. Cancer Res. 2010 Jan 01; 70(1):329-37. Chow KH, Sun RW, Lam JB, Li CK, Xu A, Ma DL, Abagyan R, Wang Y, Che CM. PMID: 19996284.
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    198. Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression. Chemistry. 2009 Dec 07; 15(47):13008-21. Wu P, Ma DL, Leung CH, Yan SC, Zhu N, Abagyan R, Che CM. PMID: 19876976.
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    199. A new method for publishing three-dimensional content. PLoS One. 2009 Oct 20; 4(10):e7394. Raush E, Totrov M, Marsden BD, Abagyan R. PMID: 19841676; PMCID: PMC2754609.
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    200. SGC--structural biology and human health: a new approach to publishing structural biology results. PLoS One. 2009 Oct 20; 4(10):e7675. Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD. PMID: 19847312; PMCID: PMC2762615.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    201. Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands. J Med Chem. 2009 Sep 24; 52(18):5635-41. Bisson WH, Koch DC, O'Donnell EF, Khalil SM, Kerkvliet NI, Tanguay RL, Abagyan R, Kolluri SK. PMID: 19719119; PMCID: PMC3289977.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansAnimalsCells
    202. FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics. 2009 Oct 01; 25(19):2544-51. Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P. PMID: 19620099; PMCID: PMC2800348.
      View in: PubMed   Mentions: 65     Fields:    
    203. Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J Mol Recognit. 2009 Jul-Aug; 22(4):307-18. Katritch V, Reynolds KA, Cherezov V, Hanson MA, Roth CB, Yeager M, Abagyan R. PMID: 19353579; PMCID: PMC2693451.
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    204. Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling. Biochemistry. 2009 Jun 16; 48(23):5303-12. Dong M, Lam PC, Pinon DI, Abagyan R, Miller LJ. PMID: 19441839; PMCID: PMC3443625.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    205. Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor. Mol Pharmacol. 2009 Aug; 76(2):264-74. Gao F, Harikumar KG, Dong M, Lam PC, Sexton PM, Christopoulos A, Bordner A, Abagyan R, Miller LJ. PMID: 19429716; PMCID: PMC2713122.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    206. Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model. 2009 Mar; 49(3):716-25. Rueda M, Bottegoni G, Abagyan R. PMID: 19434904; PMCID: PMC2891173.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    207. Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation. J Biol Chem. 2009 May 08; 284(19):13185-92. Wu YW, Goody RS, Abagyan R, Alexandrov K. PMID: 19240028; PMCID: PMC2676050.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    208. Structure-based approaches to antibiotic drug discovery. Curr Protoc Microbiol. 2009 Feb; Chapter 17:Unit17.2. Nicola G, Abagyan R. PMID: 19235149.
      View in: PubMed   Mentions: 3     Fields:    
    209. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem. 2009 Jan 22; 52(2):397-406. Bottegoni G, Kufareva I, Totrov M, Abagyan R. PMID: 19090659; PMCID: PMC2662720.
      View in: PubMed   Mentions: 75     Fields:    Translation:Cells
    210. Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J Comput Aided Mol Des. 2009 May; 23(5):273-88. Reynolds KA, Katritch V, Abagyan R. PMID: 19148767; PMCID: PMC2667566.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    211. Homology modeling of GPCRs. Methods Mol Biol. 2009; 552:97-113. Simms J, Hall NE, Lam PH, Miller LJ, Christopoulos A, Abagyan R, Sexton PM. PMID: 19513644.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    212. The flexible pocketome engine for structural chemogenomics. Methods Mol Biol. 2009; 575:249-79. Abagyan R, Kufareva I. PMID: 19727619; PMCID: PMC2975493.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    213. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem. 2008 Dec 25; 51(24):7921-32. Kufareva I, Abagyan R. PMID: 19053777; PMCID: PMC2669721.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansCells
    214. Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins. 2008 Aug 15; 72(3):848-62. Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J. PMID: 18260112; PMCID: PMC4162409.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    215. Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations. J Mol Graph Model. 2008 Nov; 27(4):452-8. Bisson WH, Abagyan R, Cavasotto CN. PMID: 18805032.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    216. Damped-dynamics flexible fitting. Biophys J. 2008 Oct; 95(7):3192-207. Kovacs JA, Yeager M, Abagyan R. PMID: 18586844; PMCID: PMC2547429.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    217. Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking. ChemMedChem. 2008 Jun; 3(6):881-4. Ma DL, Lai TS, Chan FY, Chung WH, Abagyan R, Leung YC, Wong KY. PMID: 18383062.
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    218. Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding. Mol Pharmacol. 2008 Aug; 74(2):413-22. Dong M, Lam PC, Pinon DI, Sexton PM, Abagyan R, Miller LJ. PMID: 18467541; PMCID: PMC3879803.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    219. New method for the assessment of all drug-like pockets across a structural genome. J Comput Biol. 2008 Apr; 15(3):231-40. Nicola G, Smith CA, Abagyan R. PMID: 18333758; PMCID: PMC2660599.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    220. Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model. 2008 Mar; 48(3):489-97. Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S. PMID: 18302357.
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    221. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol. 2008 Apr; 18(2):178-84. Totrov M, Abagyan R. PMID: 18302984; PMCID: PMC2396190.
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    222. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des. 2008 May; 22(5):311-25. Bottegoni G, Kufareva I, Totrov M, Abagyan R. PMID: 18273556; PMCID: PMC2641994.
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    223. Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J Med Chem. 2008 Feb 14; 51(3):581-8. Cavasotto CN, Orry AJ, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O'Neill KA, Hine H, Burton MS, Voigt JH, Abagyan RA, Bayne ML, Monsma FJ. PMID: 18198821.
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    224. 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.
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    225. Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J Comput Aided Mol Des. 2007 Oct-Nov; 21(10-11):549-58. Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan R, Hruby DE. PMID: 17960327; PMCID: PMC7087885.
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    226. De novo discovery of serotonin N-acetyltransferase inhibitors. J Med Chem. 2007 Nov 01; 50(22):5330-8. Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA. PMID: 17924613; PMCID: PMC2531295.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    227. Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. J Med Chem. 2007 Nov 01; 50(22):5357-63. Mallya M, Phillips RL, Saldanha SA, Gooptu B, Brown SC, Termine DJ, Shirvani AM, Wu Y, Sifers RN, Abagyan R, Lomas DA. PMID: 17918823; PMCID: PMC2631427.
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    228. Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem. 2007 Dec 14; 282(50):36505-13. Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, Pasquale EB, Kuhn P. PMID: 17897949; PMCID: PMC4370777.
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    229. Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. J Biol Chem. 2007 Nov 09; 282(45):32834-43. Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ. PMID: 17827151.
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    230. Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc Natl Acad Sci U S A. 2007 Jul 17; 104(29):11927-32. Bisson WH, Cheltsov AV, Bruey-Sedano N, Lin B, Chen J, Goldberger N, May LT, Christopoulos A, Dalton JT, Sexton PM, Zhang XK, Abagyan R. PMID: 17606915; PMCID: PMC1924583.
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    231. Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science. 2007 Jul 27; 317(5837):516-9. Outeiro TF, Kontopoulos E, Altmann SM, Kufareva I, Strathearn KE, Amore AM, Volk CB, Maxwell MM, Rochet JC, McLean PJ, Young AB, Abagyan R, Feany MB, Hyman BT, Kazantsev AG. PMID: 17588900.
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    232. Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys J. 2007 Sep 15; 93(6):1950-9. Kovacs JA, Yeager M, Abagyan R. PMID: 17496035; PMCID: PMC1959528.
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    233. Self-assembling cannabinomimetics: supramolecular structures of N-alkyl amides. J Nat Prod. 2007 Jun; 70(6):1010-5. Raduner S, Bisson W, Abagyan R, Altmann KH, Gertsch J. PMID: 17497806.
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    234. Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol. 2007 Aug; 72(2):280-90. Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ. PMID: 17475809.
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    235. PIER: protein interface recognition for structural proteomics. Proteins. 2007 May 01; 67(2):400-17. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. PMID: 17299750.
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    236. Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening. Biochem Biophys Res Commun. 2007 Jul 06; 358(3):686-91. Nicola G, Smith CA, Lucumi E, Kuo MR, Karagyozov L, Fidock DA, Sacchettini JC, Abagyan R. PMID: 17509532; PMCID: PMC1987361.
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    237. Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction. Biochemistry. 2007 Apr 17; 46(15):4522-31. Dong M, Ding XQ, Thomas SE, Gao F, Lam PC, Abagyan R, Miller LJ. PMID: 17381074; PMCID: PMC2580722.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    238. Molecular modeling and mutagenesis of gap junction channels. Prog Biophys Mol Biol. 2007 May-Jun; 94(1-2):15-28. Kovacs JA, Baker KA, Altenberg GA, Abagyan R, Yeager M. PMID: 17524457; PMCID: PMC2819402.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    239. DFprot: a webtool for predicting local chain deformability. Bioinformatics. 2007 Apr 01; 23(7):901-2. Garzón JI, Kovacs J, Abagyan R, Chacón P. PMID: 17277334.
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    240. Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A. Anal Chem. 2006 Dec 15; 78(24):8265-72. Saldanha SA, Kaler G, Cottam HB, Abagyan R, Taylor SS. PMID: 17165815; PMCID: PMC3435108.
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    241. ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics. 2007 Feb 15; 23(4):427-33. Garzón JI, Kovacs J, Abagyan R, Chacón P. PMID: 17150992.
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    242. The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol. 2006 Nov; 4(11):e362. Malinina L, Malakhova ML, Kanack AT, Lu M, Abagyan R, Brown RE, Patel DJ. PMID: 17105344; PMCID: PMC1618416.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    243. Weighted quality estimates in machine learning. Bioinformatics. 2006 Nov 01; 22(21):2597-603. Budagyan L, Abagyan R. PMID: 16935929.
      View in: PubMed   Mentions: 3     Fields:    
    244. Defining the CD59-C9 binding interaction. J Biol Chem. 2006 Sep 15; 281(37):27398-404. Huang Y, Qiao F, Abagyan R, Hazard S, Tomlinson S. PMID: 16844690.
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    245. Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-deficient cells. Chem Biol. 2006 Jul; 13(7):765-70. Altmann SM, Muryshev A, Fossale E, Maxwell MM, Norflus FN, Fox J, Hersch SM, Young AB, MacDonald ME, Abagyan R, Kazantsev AG. PMID: 16873024.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    246. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins. 2006 May 15; 63(3):512-26. Bordner AJ, Abagyan R. PMID: 16470819.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    247. Structure-based development of target-specific compound libraries. Drug Discov Today. 2006 Mar; 11(5-6):261-6. Orry AJ, Abagyan RA, Cavasotto CN. PMID: 16580603.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    248. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 2006 Feb 01; 78(3):779-87. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G. PMID: 16448051.
      View in: PubMed   Mentions: 2016     Fields:    Translation:HumansAnimals
    249. In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. Bioorg Med Chem Lett. 2006 Apr 01; 16(7):1969-74. Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ. PMID: 16413185.
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    250. Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci. 2006 Feb; 31(2):76-8. Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, Marsden BD. PMID: 16406633.
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    251. METLIN: a metabolite mass spectral database. Ther Drug Monit. 2005 Dec; 27(6):747-51. Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G. PMID: 16404815.
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    252. Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins. J Med Chem. 2005 Dec 01; 48(24):7781-8. Hill T, Odell LR, Edwards JK, Graham ME, McGeachie AB, Rusak J, Quan A, Abagyan R, Scott JL, Robinson PJ, McCluskey A. PMID: 16302817.
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    253. Surrogate data--a secure way to share corporate data. J Comput Aided Mol Des. 2005 Sep-Oct; 19(9-10):749-64. Tetko IV, Abagyan R, Oprea TI. PMID: 16267691.
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    254. Statistical analysis and prediction of protein-protein interfaces. Proteins. 2005 Aug 15; 60(3):353-66. Bordner AJ, Abagyan R. PMID: 15906321.
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    255. Insights into the human CD59 complement binding interface toward engineering new therapeutics. J Biol Chem. 2005 Oct 07; 280(40):34073-9. Huang Y, Smith CA, Song H, Morgan BP, Abagyan R, Tomlinson S. PMID: 16079145.
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    256. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins. 2005 Aug 01; 60(2):308-13. Fernández-Recio J, Abagyan R, Totrov M. PMID: 15981266.
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    257. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc. 2005 Jul 06; 127(26):9632-40. Cavasotto CN, Kovacs JA, Abagyan RA. PMID: 15984891.
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    258. Efficient synthetic inhibitors of anthrax lethal factor. Proc Natl Acad Sci U S A. 2005 Jul 05; 102(27):9499-504. Forino M, Johnson S, Wong TY, Rozanov DV, Savinov AY, Li W, Fattorusso R, Becattini B, Orry AJ, Jung D, Abagyan RA, Smith JW, Alibek K, Liddington RC, Strongin AY, Pellecchia M. PMID: 15983377; PMCID: PMC1160517.
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    259. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics. 2005 Jun; 4(6):752-61. An J, Totrov M, Abagyan R. PMID: 15757999.
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    260. REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics. 2005 May 15; 21(10):2315-21. Bordner AJ, Abagyan R. PMID: 15749694.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    261. Druggability of SCF ubiquitin ligase-protein interfaces. Methods Enzymol. 2005; 399:634-53. Cardozo T, Abagyan R. PMID: 16338386.
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    262. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 2005 Jan 01; 58(1):134-43. Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. PMID: 15495260.
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    263. Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins. 2004 Nov 01; 57(2):400-13. Bordner AJ, Abagyan RA. PMID: 15340927.
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    264. Predictions of protein flexibility: first-order measures. Proteins. 2004 Sep 01; 56(4):661-8. Kovacs JA, Chacón P, Abagyan R. PMID: 15281119.
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    265. Determinants of retinoid X receptor transcriptional antagonism. J Med Chem. 2004 Aug 26; 47(18):4360-72. Cavasotto CN, Liu G, James SY, Hobbs PD, Peterson VJ, Bhattacharya AA, Kolluri SK, Zhang XK, Leid M, Abagyan R, Liddington RC, Dawson MI. PMID: 15317450.
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    266. Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorg Med Chem Lett. 2004 Jun 21; 14(12):3275-8. Hill TA, Odell LR, Quan A, Abagyan R, Ferguson G, Robinson PJ, McCluskey A. PMID: 15149689.
      View in: PubMed   Mentions: 26     Fields:    Translation:Animals
    267. SAD--a normalized structural alignment database: improving sequence-structure alignments. Bioinformatics. 2004 Oct 12; 20(15):2333-44. Marsden B, Abagyan R. PMID: 15087320.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    268. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol. 2004 Mar 12; 337(1):209-25. Cavasotto CN, Abagyan RA. PMID: 15001363.
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    269. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol. 2004 Jan 16; 335(3):843-65. Fernández-Recio J, Totrov M, Abagyan R. PMID: 14687579.
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    270. Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform. 2004; 15(2):31-41. An J, Totrov M, Abagyan R. PMID: 15706489.
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    271. Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des. 2003 Nov; 17(11):755-63. Bursulaya BD, Totrov M, Abagyan R, Brooks CL. PMID: 15072435.
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    272. Nuclear hormone receptor targeted virtual screening. J Med Chem. 2003 Jul 03; 46(14):3045-59. Schapira M, Abagyan R, Totrov M. PMID: 12825943.
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    273. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins. 2003 Jul 01; 52(1):113-7. Fernández-Recio J, Totrov M, Abagyan R. PMID: 12784376.
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    274. Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A. 2003 Jun 10; 100(12):7354-9. Schapira M, Raaka BM, Das S, Fan L, Totrov M, Zhou Z, Wilson SR, Abagyan R, Samuels HH. PMID: 12777627; PMCID: PMC165879.
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    275. Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins. 2003 May 15; 51(3):423-33. Cavasotto CN, Orry AJ, Abagyan RA. PMID: 12696053.
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    276. Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel. 2003 May; 6(3):339-45. Zhou Y, Abagyan R. PMID: 12833666.
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    277. The transthyretin-related protein family. Eur J Biochem. 2003 Feb; 270(3):518-32. Eneqvist T, Lundberg E, Nilsson L, Abagyan R, Sauer-Eriksson AE. PMID: 12542701.
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    278. ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. J Comput Chem. 2003 Jan 30; 24(2):254-65. Katritch V, Totrov M, Abagyan R. PMID: 12497604.
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    279. Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science. 2002 Oct 04; 298(5591):216-8. Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, Winzeler EA. PMID: 12364807.
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    280. Soft protein-protein docking in internal coordinates. Protein Sci. 2002 Feb; 11(2):280-91. Fernández-Recio J, Totrov M, Abagyan R. PMID: 11790838; PMCID: PMC2373434.
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    281. Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics. 2002; 3:3. Zhou Y, Abagyan R. PMID: 11835687; PMCID: PMC65509.
      View in: PubMed   Mentions: 24     Fields:    
    282. Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol. 2002; 2:1. Schapira M, Abagyan R, Totrov M. PMID: 11860617; PMCID: PMC65631.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    283. Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput. 2002; 552-63. Fernandez-Recio J, Totrov M, Abagyan R. PMID: 11928507.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    284. Computational structural proteomics. Ernst Schering Res Found Workshop. 2002; (38):149-66. Brive L, Abagyan R. PMID: 12061000.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    285. High-throughput docking for lead generation. Curr Opin Chem Biol. 2001 Aug; 5(4):375-82. Abagyan R, Totrov M. PMID: 11470599.
      View in: PubMed   Mentions: 70     Fields:    Translation:Cells
    286. In silico discovery of novel retinoic acid receptor agonist structures. BMC Struct Biol. 2001; 1:1. Schapira M, Raaka BM, Samuels HH, Abagyan R. PMID: 11405897; PMCID: PMC32304.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    287. Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity. Proteins. 2001 Feb 15; 42(3):383-9. Norledge BV, Lambeir AM, Abagyan RA, Rottmann A, Fernandez AM, Filimonov VV, Peter MG, Wierenga RK. PMID: 11151009.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    288. Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide. Biopolymers. 2001; 60(2):124-33. Totrov M, Abagyan R. PMID: 11455546.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    289. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J Comput Aided Mol Des. 2000 Aug; 14(6):593-610. Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL. PMID: 10921774.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    290. Antibodies against thrombospondin-related anonymous protein do not inhibit Plasmodium sporozoite infectivity in vivo. Infect Immun. 2000 Jun; 68(6):3667-73. Gantt S, Persson C, Rose K, Birkett AJ, Abagyan R, Nussenzweig V. PMID: 10816526; PMCID: PMC97657.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCellsPHPublic Health
    291. Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition. J Mol Biol. 2000 Apr 21; 298(1):95-110. Jin E, Katritch V, Olson WK, Kharatisvili M, Abagyan R, Pilch DS. PMID: 10756107.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    292. Genetic linkage mapping of zebrafish genes and ESTs. Genome Res. 2000 Apr; 10(4):558-67. Kelly PD, Chu F, Woods IG, Ngo-Hazelett P, Cardozo T, Huang H, Kimm F, Liao L, Yan YL, Zhou Y, Johnson SL, Abagyan R, Schier AF, Postlethwait JH, Talbot WS. PMID: 10779498; PMCID: PMC310859.
      View in: PubMed   Mentions: 35     Fields:    Translation:Animals
    293. Expression of the adenovirus receptor and its interaction with the fiber knob. Exp Cell Res. 2000 Feb 25; 255(1):47-55. Tomko RP, Johansson CB, Totrov M, Abagyan R, Frisén J, Philipson L. PMID: 10666333.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    294. Rational discovery of novel nuclear hormone receptor antagonists. Proc Natl Acad Sci U S A. 2000 Feb 01; 97(3):1008-13. Schapira M, Raaka BM, Samuels HH, Abagyan R. PMID: 10655475; PMCID: PMC15503.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    295. Estimating local backbone structural deviation in homology models. Comput Chem. 2000 Jan; 24(1):13-31. Cardozo T, Batalov S, Abagyan R. PMID: 10642877.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    296. NRIF3 is a novel coactivator mediating functional specificity of nuclear hormone receptors. Mol Cell Biol. 1999 Oct; 19(10):7191-202. Li D, Desai-Yajnik V, Lo E, Schapira M, Abagyan R, Samuels HH. PMID: 10490654; PMCID: PMC84712.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    297. Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics. Structure. 1999 Jun 15; 7(6):663-70. Stigler RD, Hoffmann B, Abagyan R, Schneider-Mergener J. PMID: 10404595.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    298. Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit. 1999 May-Jun; 12(3):177-90. Schapira M, Totrov M, Abagyan R. PMID: 10398408.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansCells
    299. Identification of the individual residues that determine human CD59 species selective activity. J Biol Chem. 1999 Apr 16; 274(16):10969-74. Zhang HF, Yu J, Chen S, Morgan BP, Abagyan R, Tomlinson S. PMID: 10196177.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    300. A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res. 1999 Apr; 9(4):334-47. Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D, Abagyan R, Schier AF, Talbot WS. PMID: 10207156.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    301. Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast. EMBO J. 1998 Sep 15; 17(18):5374-87. Isakoff SJ, Cardozo T, Andreev J, Li Z, Ferguson KM, Abagyan R, Lemmon MA, Aronheim A, Skolnik EY. PMID: 9736615; PMCID: PMC1170863.
      View in: PubMed   Mentions: 117     Fields:    Translation:AnimalsCells
    302. Novel anchorage of GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP. Neuron. 1998 Sep; 21(3):581-91. Srivastava S, Osten P, Vilim FS, Khatri L, Inman G, States B, Daly C, DeSouza S, Abagyan R, Valtschanoff JG, Weinberg RJ, Ziff EB. PMID: 9768844.
      View in: PubMed   Mentions: 112     Fields:    Translation:AnimalsCells
    303. TNF-alpha convertase enzyme from human arthritis-affected cartilage: isolation of cDNA by differential display, expression of the active enzyme, and regulation of TNF-alpha. J Immunol. 1998 May 01; 160(9):4570-9. Patel IR, Attur MG, Patel RN, Stuchin SA, Abagyan RA, Abramson SB, Amin AR. PMID: 9574564.
      View in: PubMed   Mentions: 30     Fields:    Translation:Humans
    304. How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold Des. 1998; 3(6):513-22. Zhou Y, Abagyan R. PMID: 9889165.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    305. Energy strain in three-dimensional protein structures. Fold Des. 1998; 3(4):259-69. Maiorov V, Abagyan R. PMID: 9710569.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    306. The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. J Mol Biol. 1997 Oct 31; 273(3):714-28. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK. PMID: 9402066.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    307. Do aligned sequences share the same fold? J Mol Biol. 1997 Oct 17; 273(1):355-68. Abagyan RA, Batalov S. PMID: 9367768.
      View in: PubMed   Mentions: 87     Fields:    Translation:Cells
    308. Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Sci. 1997 Oct; 6(10):2143-58. Rashin AA, Rashin BH, Rashin A, Abagyan R. PMID: 9336837; PMCID: PMC2143572.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    309. Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity. Biochemistry. 1997 Aug 05; 36(31):9423-8. Yu J, Dong S, Rushmere NK, Morgan BP, Abagyan R, Tomlinson S. PMID: 9235986.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    310. TSG101 may be the prototype of a class of dominant negative ubiquitin regulators. Nat Genet. 1997 Aug; 16(4):330-1. Koonin EV, Abagyan RA. PMID: 9241264.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansAnimalsCells
    311. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol. 1997 May 09; 268(3):678-85. Abagyan RA, Totrov MM. PMID: 9171291.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    312. A new method for modeling large-scale rearrangements of protein domains. Proteins. 1997 Mar; 27(3):410-24. Maiorov V, Abagyan R. PMID: 9094743.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    313. Mapping the active site of CD59. J Exp Med. 1997 Feb 17; 185(4):745-53. Yu J, Abagyan R, Dong S, Gilbert A, Nussenzweig V, Tomlinson S. PMID: 9034152; PMCID: PMC2196154.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    314. Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop. Protein Eng. 1997 Feb; 10(2):159-67. Thanki N, Zeelen JP, Mathieu M, Jaenicke R, Abagyan RA, Wierenga RK, Schliebs W. PMID: 9089815.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    315. Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search. Proteins. 1997; Suppl 1:29-37. Abagyan R, Batalov S, Cardozo T, Totrov M, Webber J, Zhou Y. PMID: 9485492.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    316. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins. 1997; Suppl 1:215-20. Totrov M, Abagyan R. PMID: 9485515.
      View in: PubMed   Mentions: 152     Fields:    Translation:Cells
    317. Long pentraxins: an emerging group of proteins with diverse functions. Cytokine Growth Factor Rev. 1996 Aug; 7(2):191-202. Goodman AR, Cardozo T, Abagyan R, Altmeyer A, Wisniewski HG, Vilcek J. PMID: 8899296.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    318. The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J Mol Biol. 1996 Jul 26; 260(4):588-603. Chalikian TV, Totrov M, Abagyan R, Breslauer KJ. PMID: 8759322.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    319. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol. 1996 Mar; 3(3):233-9. Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN. PMID: 8605624.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    320. The contour-buildup algorithm to calculate the analytical molecular surface. J Struct Biol. 1996 Jan-Feb; 116(1):138-43. Totrov M, Abagyan R. PMID: 8742735.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    321. Homology modeling by the ICM method. Proteins. 1995 Nov; 23(3):403-14. Cardozo T, Totrov M, Abagyan R. PMID: 8710833.
      View in: PubMed   Mentions: 84     Fields:    Translation:Cells
    322. Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8. Structure. 1995 Jul 15; 3(7):669-79. Borchert TV, Kishan KV, Zeelen JP, Schliebs W, Thanki N, Abagyan R, Jaenicke R, Wierenga RK. PMID: 8591044.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    323. Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability. Protein Eng. 1995 Mar; 8(3):249-59. Houbrechts A, Moreau B, Abagyan R, Mainfroid V, Préaux G, Lamproye A, Poncin A, Goormaghtigh E, Ruysschaert JM, Martial JA, et al. PMID: 7479687.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    324. The protein folding problem: finding a few minimums in a near infinite space. Comput Chem. 1994 Sep; 18(3):225-31. Argos P, Abagyan R. PMID: 7952893.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    325. Recognition of distantly related proteins through energy calculations. Proteins. 1994 Jun; 19(2):132-40. Abagyan R, Frishman D, Argos P. PMID: 8090707.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    326. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol. 1994 Apr; 1(4):259-63. Totrov M, Abagyan R. PMID: 7656055.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    327. Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc Natl Acad Sci U S A. 1994 Feb 15; 91(4):1515-8. Borchert TV, Abagyan R, Jaenicke R, Wierenga RK. PMID: 8108439; PMCID: PMC43190.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    328. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol. 1994 Jan 21; 235(3):983-1002. Abagyan R, Totrov M. PMID: 8289329.
      View in: PubMed   Mentions: 374     Fields:    Translation:Cells
    329. A technique for identifying atoms from a screen image. J Mol Graph. 1993 Dec; 11(4):245-7. Kuznetsov DA, Abagyan RA. PMID: 8136327.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    330. The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. Structure. 1993 Nov 15; 1(3):205-13. Borchert TV, Abagyan R, Kishan KV, Zeelen JP, Wierenga RK. PMID: 16100954.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    331. Towards protein folding by global energy optimization. FEBS Lett. 1993 Jun 28; 325(1-2):17-22. Abagyan RA. PMID: 8513887.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    332. A method to configure protein side-chains from the main-chain trace in homology modelling. J Mol Biol. 1993 Jun 05; 231(3):849-60. Eisenmenger F, Argos P, Abagyan R. PMID: 8515455.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    333. Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Eng. 1993 Jan; 6(1):41-50. Gibson TJ, Thompson JD, Abagyan RA. PMID: 8433970.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    334. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J Mol Biol. 1992 May 20; 225(2):519-32. Abagyan R, Argos P. PMID: 1593634.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    335. Electrophoretic behavior of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n and implications for a DNA bending model. Nucleic Acids Res. 1990 Feb 25; 18(4):989-92. Abagyan RA, Mironov VN, Chernov BK, Chuprina VP, Ulyanov AV. PMID: 2315048; PMCID: PMC330354.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    336. Sequence dependent modulating effect of camptothecin on the DNA-cleaving activity of the calf thymus type I topoisomerase. Nucleic Acids Res. 1990 Feb 11; 18(3):637-45. Gromova II, Buchman VL, Abagyan RA, Ulyanov AV, Bronstein IB. PMID: 2155407; PMCID: PMC333473.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    337. Structure of the hydration shells of oligo(dA-dT).oligo(dA-dT) and oligo(dA).oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations. Biopolymers. 1990; 30(5-6):563-81. Eisenhaber F, Tumanyan VG, Abagyan RA. PMID: 2265229.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    338. An automatic search for similar spatial arrangements of alpha-helices and beta-strands in globular proteins. J Biomol Struct Dyn. 1989 Jun; 6(6):1045-60. Abagyan RA, Maiorov VN. PMID: 2818856.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    339. New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures. J Biomol Struct Dyn. 1989 Feb; 6(4):815-32. Mazur AK, Abagyan RA. PMID: 2619942.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    340. New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles. J Biomol Struct Dyn. 1989 Feb; 6(4):833-45. Abagyan RA, Mazur AK. PMID: 2619943.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    341. Structural basis of stable bending in DNA containing An tracts. Different types of bending. J Biomol Struct Dyn. 1988 Aug; 6(1):121-38. Chuprina VP, Abagyan RA. PMID: 3271514.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    342. A simple qualitative representation of polypeptide chain folds: comparison of protein tertiary structures. J Biomol Struct Dyn. 1988 Jun; 5(6):1267-79. Abagyan RA, Maiorov VN. PMID: 3271511.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    343. Anomalous properties of adenine.thymine tracts. Nature. 1988 Mar 10; 332(6160):117. Chuprina VP, Abagyan RA. PMID: 3347251.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    344. [Block improvement of the genetic text as a factor of acceleration of biological evolution]. Biofizika. 1985 May-Jun; 30(3):418-21. Ivanitskii GR, Esipova NG, Abagyan RA, Shnol' SE. PMID: 4027270.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    345. [Two types of tripeptide conformation in collagen. Calculation of the structure of (Gly-Pro-Ser)n and (Gly-Val-Hyp)n polytripeptides]. Bioorg Khim. 1984 Apr; 10(4):476-82. Abagyan RA, Tumanian VG, Esipova NG. PMID: 6548632.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    346. [Arrangement of molecular packing of collagen in fibrils]. Biofizika. 1983 May-Jun; 28(3):498-500. Abagyan RA. PMID: 6871272.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    347. [Diffraction from the alternating helix]. Biofizika. 1983 May-Jun; 28(3):388-92. Abagyan RA. PMID: 6871260.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    348. [Diffraction effects on x-rays of the oligotripeptide (Gly-Pro-Pro)10, isomorphic to collagen]. Biofizika. 1981 Jul-Aug; 26(4):734-6. Rogulenkova VN, Abagyan RA, Tumanian VG, Esipova NG. PMID: 7284464.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
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