Publications
List of publications:
1: Makunts T, Joulfayan H, Abagyan R. 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 1;5:e55976. doi: 10.2196/55976. PMID: 38738836.
3: Munson BP, Chen M, Bogosian A, Kreisberg JF, Licon K, Abagyan R, Kuenzi BM, Ideker T. De novo generation of multi-target compounds using deep generative chemistry. Nat Commun. 2024 May 6;15(1):3636. doi: 10.1038/s41467-024-47120-y. PMID: 38710699; PMCID: PMC11074339.
4: Raush E, Abagyan R, Totrov M. 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. doi:10.1021/acs.jctc.4c00280. Epub 2024 Apr 26. PMID: 38669307.
5: Makunts T, Grabska S, Grabski H, Abagyan R. Co-occurring infections in cancer patients treated with checkpoint inhibitors significantly increase the risk of immune related adverse events. medRxiv [Preprint]. 2024 Feb 15:2024.02.14.24302840. doi: 10.1101/2024.02.14.24302840. PMID: 38405974; PMCID: PMC10889010.
7: 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. Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. Cell Genom. 2023 May 30;3(7):100339. doi: 10.1016/j.xgen.2023.100339. PMID: 37492105; PMCID: PMC10363808.
8: Joulfayan H, Makunts T, Abagyan R. Anti-TNF-α therapy induced psoriasis in rheumatoid arthritis patients according to FDA postmarketing surveillance data. Sci Rep. 2023 Jun 27;13(1):10448. doi: 10.1038/s41598-023-37010-6. PMID: 37369753; PMCID: PMC10300095.
9: Makunts T, Dahill D, Jerome L, de Boer A, Abagyan R. Concomitant medications associated with ischemic, hypertensive, and arrhythmic events in MDMA users in FDA adverse event reporting system. Front Psychiatry. 2023 May 18;14:1149766. doi: 10.3389/fpsyt.2023.1149766. PMID: 37275981; PMCID: PMC10233020.
10: Meewan I, Shiryaev SA, Kattoula J, Huang CT, Lin V, Chuang CH, Terskikh AV, Abagyan R. Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in "Super-Open" Conformation. Viruses. 2023 Apr 30;15(5):1106. doi: 10.3390/v15051106. PMID: 37243192; PMCID: PMC10224173.
11: Sauvey C, Meewan I, Ehrenkaufer G, Blevitt J, Jackson P, Abagyan R. High- throughput phenotypic screen identifies a new family of potent anti-amoebic compounds. PLoS One. 2023 May 9;18(5):e0280232. doi: 10.1371/journal.pone.0280232. PMID: 37159460; PMCID: PMC10168566.
12: Raush E, Abagyan R, Totrov M. 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. doi: 10.1021/acs.jcim.2c00790. Epub 2022 Dec 1. PMID: 36456533.
13: Awdishu L, Abagyan R. Do Proton-Pump Inhibitors Cause CKD and Progression of CKD?: PRO. Kidney360. 2022 Jan 4;3(7):1134-1136. doi: 10.34067/KID.0007622021. PMID: 35919519; PMCID: PMC9337907.
14: 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. Discovery of Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L. Pharmaceuticals (Basel). 2022 Jun 13;15(6):744. doi: 10.3390/ph15060744. PMID: 35745663; PMCID: PMC9230533.
15: Bartholow TG, Sztain T, Young MA, Lee DJ, Davis TD, Abagyan R, Burkart MD. Control of Unsaturation in De Novo Fatty Acid Biosynthesis by FabA. Biochemistry. 2022 Apr 5;61(7):608-615. doi: 10.1021/acs.biochem.2c00094. PMID: 35255690; PMCID: PMC9769579.
16: Rosenthal SB, Wang H, Shi D, Liu C, Abagyan R, McEvoy LK, Chen CH. Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics. PLoS Comput Biol. 2022 Feb 25;18(2):e1009903. doi: 10.1371/journal.pcbi.1009903. PMID: 35213535; PMCID: PMC8906581.
17: Makunts T, Burkhart K, Abagyan R, Lee P. Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events. PLoS One. 2022 Feb 10;17(2):e0263402. doi: 10.1371/journal.pone.0263402. PMID: 35143542; PMCID: PMC8830697.
18: Makunts T, Jerome L, Abagyan R, de Boer A. Reported Cases of Serotonin Syndrome in MDMA Users in FAERS Database. Front Psychiatry. 2022 Jan 24;12:824288. doi: 10.3389/fpsyt.2021.824288. PMID: 35140642; PMCID: PMC8820588.
19: 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. ARN25068, a versatile starting point towards triple GSK-3β/FYN/DYRK1A inhibitors to tackle tau-related neurological disorders. Eur J Med Chem. 2022 Feb 5;229:114054. doi: 10.1016/j.ejmech.2021.114054. Epub 2021 Dec 16. PMID: 34959172; PMCID: PMC9704499.
20: Wollmer MA, Makunts T, Krüger THC, Abagyan R. Postmarketing safety surveillance data reveals protective effects of botulinum toxin injections against incident anxiety. Sci Rep. 2021 Dec 21;11(1):24173. doi:
10.1038/s41598-021-03713-x. PMID: 34934096; PMCID: PMC8692576.
21: Keshishi D, Makunts T, Abagyan R. Common osteoporosis drug associated with increased rates of depression and anxiety. Sci Rep. 2021 Dec 14;11(1):23956. doi: 10.1038/s41598-021-03214-x. PMID: 34907232; PMCID: PMC8671447.
22: Bartholow TG, Sztain T, Young MA, Davis TD, Abagyan R, Burkart MD. Protein-protein interaction based substrate control in the E. coli octanoic acid transferase, LipB. RSC Chem Biol. 2021 Jul 28;2(5):1466-1473. doi: 10.1039/d1cb00125f. PMID: 34704050; PMCID: PMC8495967.
23: Nigam AK, Ojha AA, Li JG, Shi D, Bhatnagar V, Nigam KB, Abagyan R, Nigam SK. 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):1720. doi:10.3390/pharmaceutics13101720. PMID: 34684013; PMCID: PMC8538396.
24: 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. Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Comput Biol. 2021 Sep 14;17(9):e1009302. doi: 10.1371/journal.pcbi.1009302. PMID: 34520464; PMCID: PMC8483411.
25: Makunts T, Saunders IM, Cohen IV, Li M, Moumedjian T, Issa MA, Burkhart K, Lee P, Patel SP, Abagyan R. Myocarditis occurrence with cancer immunotherapy across indications in clinical trial and post-marketing data. Sci Rep. 2021 Aug 30;11(1):17324. doi: 10.1038/s41598-021-96467-5. PMID: 34462476; PMCID: PMC8405813.
26: Bartholow TG, Sztain T, Patel A, Lee DJ, Young MA, Abagyan R, Burkart MD.
Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis. Commun Biol. 2021 Mar 16;4(1):340. doi:
10.1038/s42003-021-01838-3. PMID: 33727677; PMCID: PMC7966745.
27: Cohen IV, Makunts T, Abagyan R, Thomas K. Concomitant drugs associated with increased mortality for MDMA users reported in a drug safety surveillance database. Sci Rep. 2021 Mar 16;11(1):5997. doi: 10.1038/s41598-021-85389-x. PMID: 33727616; PMCID: PMC7966744.
29: Natala SR, Habas A, Stocking EM, Orry A, Price DL, Gill MB, Bonhaus DW,
Abagyan R, Wrasidlo W. Structure based design and synthesis of novel Toll-like Receptor 2 (TLR 2) lipid antagonists. Bioorg Med Chem Lett. 2021 May 15;40:127861. doi: 10.1016/j.bmcl.2021.127861. Epub 2021 Feb 23. PMID: 33636302.
30: Sauvey C, Ehrenkaufer G, Shi D, Debnath A, Abagyan R. Antineoplastic kinase inhibitors: A new class of potent anti-amoebic compounds. PLoS Negl Trop Dis. 2021 Feb 8;15(2):e0008425. doi: 10.1371/journal.pntd.0008425. PMID: 33556060; PMCID: PMC7895358.
31: Nguyen VN, Abagyan R, Tsunoda SM. Mtor inhibitors associated with higher cardiovascular adverse events-A large population database analysis. Clin Transplant. 2021 Apr;35(4):e14228. doi: 10.1111/ctr.14228. Epub 2021 Feb 2. PMID: 33476406.
32: 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. A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Proc Natl Acad Sci U S A. 2020 Dec 8;117(49):31510-31518. doi: 10.1073/pnas.2018415117. Epub 2020 Nov 23. PMID: 33229576; PMCID: PMC7733821.
33: Cohen IV, Makunts T, Moumedjian T, Issa MA, Abagyan R. Cardiac adverse
events associated with chloroquine and hydroxychloroquine exposure in 20 years of drug safety surveillance reports. Sci Rep. 2020 Nov 5;10(1):19199. doi: 10.1038/s41598-020-76258-0. PMID: 33154498; PMCID: PMC7644696.
34: Poretsky E, Dressano K, Weckwerth P, Ruiz M, Char SN, Shi D, Abagyan R, Yang B, Huffaker A. Differential activities of maize plant elicitor peptides as mediators of immune signaling and herbivore resistance. Plant J. 2020 Dec;104(6):1582-1602. doi: 10.1111/tpj.15022. Epub 2020 Dec 2. PMID: 33058410.
35: He X, Feng J, Yan S, Zhang Y, Zhong C, Liu Y, Shi D, Abagyan R, Xiang T,
Zhang J. Biomimetic microbioreactor-supramolecular nanovesicles improve enzyme therapy of hepatic cancer. Nanomedicine. 2021 Jan;31:102311. doi: 10.1016/j.nano.2020.102311. Epub 2020 Oct 1. PMID: 33011392.
36: Hahn HJ, Abagyan R, Podust LM, Roy S, Ali IKM, Debnath A. HMG-CoA Reductase Inhibitors as Drug Leads against Naegleria fowleri. ACS Chem Neurosci. 2020 Oct 7;11(19):3089-96. doi:10.1021/acschemneuro.0c00428. Epub 2020 Sep 19. PMID: 32881478; PMCID: PMC7544672.
37: 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. Synthesis, Optimization, Antifungal Activity, Selectivity, and CYP51 Binding of New 2-Aryl-3-azolyl-1 indolyl-propan-2-ols. Pharmaceuticals (Basel). 2020 Aug 8;13(8):186. doi: 10.3390/ph13080186. PMID: 32784450; PMCID: PMC7464559.
38: Makunts T, Wollmer MA, Abagyan R. Postmarketing safety surveillance data reveals antidepressant effects of botulinum toxin across various indications and injection sites. Sci Rep. 2020 Jul 30;10(1):12851. doi:
10.1038/s41598-020-69773-7. PMID: 32732918; PMCID: PMC7393507.
39: Yang L, Zhang Y, Xie J, Zhong C, He D, Wang T, Li K, Li Y, Shi D, Abagyan R,
Yang L, Zhang J. 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. doi: 10.1039/d0nr02651d. PMID: 32639489.
40: 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. Biomimetic Membrane-Structured Nanovesicles Carrying a Supramolecular Enzyme to Cure Lung Cancer. ACS Appl Mater Interfaces. 2020 Jul 15;12(28):31112-31123. doi: 10.1021/acsami.0c06207. Epub 2020 Jun 29. PMID: 32544316.
41: 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. 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. doi: 10.1039/d0nr02588g. PMID: 32478361.
42: Makunts T, Abagyan R. How can proton pump inhibitors damage central and peripheral nervous systems? Neural Regen Res. 2020 Nov;15(11):2041-2042. doi: 10.4103/1673-5374.282252. PMID: 32394957; PMCID: PMC7716020.
43: Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM, Kufareva I. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol. 2020 Apr 9;18(4):e3000656. doi: 10.1371/journal.pbio.3000656. PMID: 32271748; PMCID: PMC7173943.
44: Engelhart DC, Granados JC, Shi D, Saier Jr MH Jr, Baker ME, Abagyan R, Nigam SK. Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs. Int J Mol Sci. 2020 Mar 5;21(5):1791. doi: 10.3390/ijms21051791. PMID: 32150922; PMCID: PMC7084758.
45: Nicola G, Kufareva I, Ilatovskiy AV, Abagyan R. Druggable exosites of the
human kino-pocketome. J Comput Aided Mol Des. 2020 Mar;34(3):219-230. doi:10.1007/s10822-019-00276-y. Epub 2020 Jan 10. PMID: 31925639; PMCID: PMC7082431.
46: Nigam AK, Li JG, Lall K, Shi D, Bush KT, Bhatnagar V, Abagyan R, Nigam SK.
Unique metabolite preferences of the drug transporters OAT1 and OAT3 analyzed by machine learning. J Biol Chem. 2020 Feb 14;295(7):1829 1842. doi: 10.1074/jbc.RA119.010729. Epub 2020 Jan 2. PMID: 31896576; PMCID: PMC7029110.
47: Graña E, Díaz-Tielas C, Sánchez-Moreiras AM, Reigosa MJ, Celeiro M, Abagyan R, Teijeira M, Duke MV, Clerk T, Pan Z, Duke SO. Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins. Physiol Plant. 2020 May;169(1):99-109. doi: 10.1111/ppl.13055. Epub 2020 Feb 24. PMID:
31828797.
48: Makunts T, Alpatty S, Lee KC, Atayee RS, Abagyan R. Proton-pump inhibitor use is associated with a broad spectrum of neurological adverse events including impaired hearing, vision, and memory. Sci Rep. 2019 Nov 21;9(1):17280. doi: 10.1038/s41598-019-53622-3. PMID: 31754136; PMCID: PMC6872761.
49: 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. Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors. Sci Rep. 2019 Nov 4;9(1):15893. doi: 10.1038/s41598-019-52141-5. PMID: 31685885; PMCID: PMC6828666.
50: Meewan I, Zhang X, Roy S, Ballatore C, O'Donoghue AJ, Schooley RT, Abagyan
R. Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant. ACS Omega. 2019 Oct 2;4(16):16999-17008. doi: 10.1021/acsomega.9b02491. PMID: 31646247; PMCID: PMC6796237.
51: Maccesi M, Aguiar PHN, Pasche V, Padilla M, Suzuki BM, Montefusco S, Abagyan R, Keiser J, Mourão MM, Caffrey CR. Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery. Parasit Vectors. 2019 Oct 22;12(1):493. doi: 10.1186/s13071-019-3747-6. PMID: 31640761; PMCID: PMC6805474.
52: Lam PC, Abagyan R, Totrov M. Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. J Comput Aided Mol Des. 2019 Dec;33(12):1057-1069. doi: 10.1007/s10822-019-00225-9. PMID:
31598897.
53: Shi D, Chahal KK, Oto P, Nothias LF, Debnath A, McKerrow JH, Podust LM,
Abagyan R. 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 Dec 13;5(12):2029-2038. doi: 10.1021/acsinfecdis.9b00227. Epub 2019 Oct 17. PMID: 31583882; PMCID: PMC7085920.
54: Escher BI, Abagyan R, Embry M, Klüver N, Redman AD, Zarfl C, Parkerton TF.
Recommendations for Improving Methods and Models for Aquatic Hazard Assessment of Ionizable Organic Chemicals. Environ Toxicol Chem. 2020 Feb;39(2):269-286. doi: 10.1002/etc.4602. PMID: 31569266.
55: Chahal KK, Li J, Kufareva I, Parle M, Durden DL, Wechsler-Reya RJ, Chen CC,
Abagyan R. Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma. PLoS One. 2019 Sep 20;14(9):e0214901. doi: 10.1371/journal.pone.0214901. PMID: 31539380; PMCID: PMC6754133.
56: Makunts T, U A, Atayee RS, Abagyan R. Retrospective analysis reveals
significant association of hypoglycemia with tramadol and methadone in contrast to other opioids. Sci Rep. 2019 Aug 28;9(1):12490. doi:
10.1038/s41598-019-48955-y. PMID: 31462666; PMCID: PMC6713717.
57: Chahal KK, Parle M, Abagyan R. Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells. ACS Omega. 2018 Sep 26;3(9):12019 12025. doi: 10.1021/acsomega.8b01864. PMID: 31459282; PMCID: PMC6645496.
58: Zhang Y, Shi D, Abagyan R, Dai W, Dong M. 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. doi: 10.1007/s12539-019-00335-w. Epub 2019 May 20. PMID: 31106388; PMCID: PMC7172024.
59: Shi D, Khan F, Abagyan R. Extended Multitarget Pharmacology of Anticancer Drugs. J Chem Inf Model. 2019 Jun 24;59(6):3006-3017. doi:
10.1021/acs.jcim.9b00031. Epub 2019 May 3. PMID: 31025863; PMCID: PMC7100364.
60: Makunts T, Cohen IV, Awdishu L, Abagyan R. Analysis of postmarketing safety data for proton-pump inhibitors reveals increased propensity for renal injury, electrolyte abnormalities, and nephrolithiasis. Sci Rep. 2019 Feb 19;9(1):2282. doi: 10.1038/s41598-019-39335-7. PMID: 30783195; PMCID: PMC6381091.
61: 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. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. J Med Chem. 2019 Feb 28;62(4):1803-1816. doi: 10.1021/acs.jmedchem.8b01766. Epub 2019 Feb 18. PMID: 30689953; PMCID: PMC7667462.
62: Bestgen B, Kufareva I, Seetoh W, Abell C, Hartmann RW, Abagyan R, Le Borgne M, Filhol O, Cochet C, Lomberget T, Engel M. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action. J Med Chem. 2019 Feb 28;62(4):1817-1836. doi: 10.1021/acs.jmedchem.8b01765. Epub 2019 Feb 13. PMID: 30689946; PMCID: PMC7579840.
63: Desai AJ, Mechin I, Nagarajan K, Valant C, Wootten D, Lam PCH, Orry A,
Abagyan R, Nair A, Sexton PM, Christopoulos A, Miller LJ. Molecular Basis of
Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor. Mol Pharmacol. 2019 Mar;95(3):245-259. doi: 10.1124/mol.118.114082. Epub 2018 Dec 27. PMID: 30591538.
64: Lam PC, Abagyan R, Totrov M. Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. J Comput Aided Mol Des. 2019 Jan;33(1):35-46. doi:
10.1007/s10822-018-0139-5. Epub 2018 Aug 9. PMID: 30094533.
65: Svetlov D, Shi D, Twentyman J, Nedialkov Y, Rosen DA, Abagyan R,
Artsimovitch I. In silico discovery of small molecules that inhibit RfaH
recruitment to RNA polymerase. Mol Microbiol. 2018 Oct;110(1):128-142. doi: 10.1111/mmi.14093. Epub 2018 Oct 2. PMID: 30069925; PMCID: PMC6595482.
66: Arnautova YA, Abagyan R, Totrov M. Protein-RNA Docking Using ICM. J Chem Theory Comput. 2018 Sep 11;14(9):4971-4984. doi: 10.1021/acs.jctc.8b00293. Epub 2018 Aug 9. PMID: 30016588.
67: Makunts T, Cohen IV, Lee KC, Abagyan R. Population scale retrospective
analysis reveals distinctive antidepressant and anxiolytic effects of
diclofenac, ketoprofen and naproxen in patients with pain. PLoS One. 2018 Apr 18;13(4):e0195521. doi: 10.1371/journal.pone.0195521. PMID: 29668764; PMCID: PMC5905979.
68: Chahal KK, Parle M, Abagyan R. Hedgehog pathway and smoothened inhibitors in cancer therapies. Anticancer Drugs. 2018 Jun;29(5):387-401. doi: 10.1097/CAD.0000000000000609. PMID: 29537987.
69: Naz S, Farooq U, Ali S, Sarwar R, Khan S, Abagyan R. Identification of new
benzamide inhibitor against α-subunit of tryptophan synthase from Mycobacterium tuberculosis through structure-based virtual screening, anti-tuberculosis activity and molecular dynamics simulations. J Biomol Struct Dyn. 2019 Mar;37(4):1043-1053. doi: 10.1080/07391102.2018.1448303. Epub 2018 Mar 13. PMID: 29502488.
70: Kauppi K, Rosenthal SB, Lo MT, Sanyal N, Jiang M, Abagyan R, McEvoy LK,
Andreassen OA, Chen CH. Revisiting Antipsychotic Drug Actions Through Gene Networks Associated With Schizophrenia. Am J Psychiatry. 2018 Jul
1;175(7):674-682. doi: 10.1176/appi.ajp.2017.17040410. Epub 2018 Mar 2. PMID:
29495895; PMCID: PMC6028303.
71: Debnath A, Calvet CM, Jennings G, Zhou W, Aksenov A, Luth MR, Abagyan R, Nes WD, McKerrow JH, Podust LM. CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM). PLoS Negl Trop Dis. 2017 Dec 28;11(12):e0006104. doi: 10.1371/journal.pntd.0006104. PMID: 29284029; PMCID: PMC5746216.
72: Schlessinger A, Abagyan R, Carlson HA, Dang KK, Guinney J, Cagan RL. Multi-targeting Drug Community Challenge. Cell Chem Biol. 2017 Dec
21;24(12):1434-1435. doi: 10.1016/j.chembiol.2017.12.006. PMID: 29272700.
73: Chan JD, Cupit PM, Gunaratne GS, McCorvy JD, Yang Y, Stoltz K, Webb TR, Dosa PI, Roth BL, Abagyan R, Cunningham C, Marchant JS. The anthelmintic praziquantel is a human serotoninergic G-protein-coupled receptor ligand. Nat Commun. 2017 Dec 5;8(1):1910. doi: 10.1038/s41467-017-02084-0. PMID: 29208933; PMCID: PMC5716991.
76: Naz S, Ngo T, Farooq U, Abagyan R. Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens. PeerJ. 2017 Sep 19;5:e3765. doi: 10.7717/peerj.3765. PMID: 28948099; PMCID: PMC5609521.
77: Lam PC, Abagyan R, Totrov M. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. J Comput Aided Mol Des. 2018 Jan;32(1):187-198. doi: 10.1007/s10822-017-0058-x. PMID: 28887659; PMCID: PMC5767200.
78: Long T, Rojo-Arreola L, Shi D, El-Sakkary N, Jarnagin K, Rock F, Meewan M,
Rascón AA Jr, Lin L, Cunningham KA, Lemieux GA, Podust L, Abagyan R, Ashrafi K, McKerrow JH, Caffrey CR. Phenotypic, chemical and functional characterization of cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential anthelmintic drug target. PLoS Negl Trop Dis. 2017 Jul 13;11(7):e0005680. doi: 10.1371/journal.pntd.0005680. PMID: 28704396; PMCID: PMC5526615.
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82: Cohen IV, Makunts T, Atayee R, Abagyan R. Population scale data reveals the
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83: Subbotina A, Ravna AW, Lysaa RA, Abagyan R, Bugno R, Sager G. Inhibition of
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84: Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S,
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115: Mayevu NM, Choe H, Abagyan R, Seong JY, Millar RP, Katz AA, Flanagan CA.
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125: McRobb FM, Kufareva I, Abagyan R. In silico identification and
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126: Wang Y, Chan FY, Sun N, Lui HK, So PK, Yan SC, Chan KF, Chiou J, Chen S,
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128: Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K,
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140: Toneff T, Funkelstein L, Mosier C, Abagyan A, Ziegler M, Hook V. Beta-
amyloid peptides undergo regulated co-secretion with neuropeptide and
catecholamine neurotransmitters. Peptides. 2013 Aug;46:126-35. doi:
10.1016/j.peptides.2013.04.020. Epub 2013 Jun 6. PMID: 23747840; PMCID:
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141: Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg
J. Viral infection controlled by a calcium-dependent lipid-binding module in
ALIX. Dev Cell. 2013 May 28;25(4):364-73. doi: 10.1016/j.devcel.2013.04.003.
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142: Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC,
Abagyan R, Handel TM. A novel approach to quantify G-protein-coupled receptor
dimerization equilibrium using bioluminescence resonance energy transfer.
Methods Mol Biol. 2013;1013:93-127. doi: 10.1007/978-1-62703-426-5_7. PMID:
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143: Vařeková RS, Geidl S, Ionescu CM, Skřehota O, Bouchal T, Sehnal D, Abagyan
R, Koča J. Predicting p Ka values from EEM atomic charges. J Cheminform. 2013
Apr 10;5(1):18. doi: 10.1186/1758-2946-5-18. PMID: 23574978; PMCID: PMC3663834.
144: Gabrielsen M, Wołosewicz 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. Synthesis,
antidepressant evaluation and docking studies of long-chain alkylnitroquipazines
as serotonin transporter inhibitors. Chem Biol Drug Des. 2013 Jun;81(6):695-706.
doi: 10.1111/cbdd.12116. Epub 2013 Apr 11. PMID: 23574807; PMCID: PMC3665732.
145: Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan
R, Mensa-Wilmot K. Lapatinib-binding protein kinases in the African trypanosome:
identification of cellular targets for kinase-directed chemical scaffolds. PLoS
One. 2013;8(2):e56150. doi: 10.1371/journal.pone.0056150. Epub 2013 Feb 20.
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146: 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,
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of Chemicals. Green Chem. 2013 Jan;15(1):181-198. doi: 10.1039/C2GC35055F. PMID:
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147: Stevens RC, Cherezov V, Katritch V, Abagyan R, Kuhn P, Rosen H, Wüthrich K.
The GPCR Network: a large-scale collaboration to determine human GPCR structure
and function. Nat Rev Drug Discov. 2013 Jan;12(1):25-34. doi: 10.1038/nrd3859.
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148: Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R. Compound activity prediction
using models of binding pockets or ligand properties in 3D. Curr Top Med Chem.
2012;12(17):1869-82. doi: 10.2174/156802612804547335. PMID: 23116466; PMCID:
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149: Montaner S, Kufareva I, Abagyan R, Gutkind JS. Molecular mechanisms
deployed by virally encoded G protein-coupled receptors in human diseases. Annu
Rev Pharmacol Toxicol. 2013;53:331-54. doi: 10.1146/annurev-
pharmtox-010510-100608. Epub 2012 Oct 22. PMID: 23092247; PMCID: PMC4074518.
150: Dong M, Xu X, Ball AM, Makhoul JA, Lam PC, Pinon DI, Orry A, Sexton PM,
Abagyan R, Miller LJ. 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. doi: 10.1096/fj.12-212399. Epub
2012 Sep 10. PMID: 22964305; PMCID: PMC3509059.
151: Wein AN, Williams BN, Liu S, Ermolinsky B, Provenzano D, Abagyan R, Orry A,
Leppla SH, Peredelchuk M. Small molecule inhibitors of Bacillus anthracis
protective antigen proteolytic activation and oligomerization. J Med Chem. 2012
Sep 27;55(18):7998-8006. doi: 10.1021/jm300804e. Epub 2012 Sep 18. PMID:
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152: Rueda M, Totrov M, Abagyan R. ALiBERO: evolving a team of complementary
pocket conformations rather than a single leader. J Chem Inf Model. 2012 Oct
22;52(10):2705-14. doi: 10.1021/ci3001088. Epub 2012 Sep 17. PMID: 22947092;
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153: Olechnovič K, Kulberkytė E, Venclovas C. CAD-score: a new contact area
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2013 Jan;81(1):149-62. doi: 10.1002/prot.24172. Epub 2012 Sep 29. PMID:
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154: Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DS, Ma VP, Abagyan R, Wong CY, Ma
DL. A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl.
2012 Sep 3;51(36):9010-4. doi: 10.1002/anie.201202937. Epub 2012 Jul 13. PMID:
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155: Neves MA, Totrov M, Abagyan R. Docking and scoring with ICM: the
benchmarking results and strategies for improvement. J Comput Aided Mol Des.
2012 Jun;26(6):675-86. doi: 10.1007/s10822-012-9547-0. Epub 2012 May 9. PMID:
22569591; PMCID: PMC3398187.
156: Chan FY, Neves MA, Sun N, Tsang MW, Leung YC, Chan TH, Abagyan R, Wong KY.
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. doi:
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157: Neves MA, Yeager M, Abagyan R. Unusual arginine formations in protein
function and assembly: rings, strings, and stacks. J Phys Chem B. 2012 Jun
14;116(23):7006-13. doi: 10.1021/jp3009699. Epub 2012 Apr 19. PMID: 22497303;
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158: Tosh DK, Phan K, Gao ZG, Gakh AA, Xu F, Deflorian F, Abagyan R, Stevens RC,
Jacobson KA, Katritch V. 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. doi: 10.1021/jm300095s. Epub
2012 Apr 30. PMID: 22486652; PMCID: PMC3479662.
159: Cawston EE, Lam PC, Harikumar KG, Dong M, Ball AM, Augustine ML, Akgün E,
Portoghese PS, Orry A, Abagyan R, Sexton PM, Miller LJ. 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. doi:
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160: Sager G, Ørvoll EØ, Lysaa RA, Kufareva I, Abagyan R, Ravna AW. 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. doi:
10.1021/jm2014666. Epub 2012 Mar 20. PMID: 22380603; PMCID: PMC4181661.
161: Orry AJ, Abagyan R. Preparation and refinement of model protein-ligand
complexes. Methods Mol Biol. 2012;857:351-73. doi: 10.1007/978-1-61779-588-6_16.
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162: Kufareva I, Abagyan R. Methods of protein structure comparison. Methods Mol
Biol. 2012;857:231-57. doi: 10.1007/978-1-61779-588-6_10. PMID: 22323224; PMCID:
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163: Katritch V, Rueda M, Abagyan R. Ligand-guided receptor optimization.
Methods Mol Biol. 2012;857:189-205. doi: 10.1007/978-1-61779-588-6_8. PMID:
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164: Jarończyk M, Wołosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP,
Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. 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. doi: 10.1016/j.ejmech.2012.01.012. Epub 2012 Jan 15. PMID:
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165: Abagyan R. Computational chemistry in 25 years. J Comput Aided Mol Des.
2012 Jan;26(1):9-10. doi: 10.1007/s10822-011-9516-z. Epub 2011 Dec 13. PMID:
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166: Kufareva I, Ilatovskiy AV, Abagyan R. Pocketome: an encyclopedia of small-
molecule binding sites in 4D. Nucleic Acids Res. 2012 Jan;40(Database
issue):D535-40. doi: 10.1093/nar/gkr825. Epub 2011 Nov 12. PMID: 22080553;
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167: Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z,
Bojarski AJ, Sylte I. Molecular mechanism of serotonin transporter inhibition
elucidated by a new flexible docking protocol. Eur J Med Chem. 2012
Jan;47(1):24-37. doi: 10.1016/j.ejmech.2011.09.056. Epub 2011 Oct 20. PMID:
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168: Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R,
Garcia-Marcos M, Ghosh P. 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. doi: 10.1126/scisignal.2002049. PMID: 21954290;
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169: Bordner AJ, Zorman B, Abagyan R. 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. doi: 10.1007/s10822-011-9470-9. Epub 2011 Sep 9. PMID:
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170: Katritch V, Abagyan R. GPCR agonist binding revealed by modeling and
crystallography. Trends Pharmacol Sci. 2011 Nov;32(11):637-43. doi:
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171: Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R; GPCR Dock 2010
participants. Status of GPCR modeling and docking as reflected by community-wide
GPCR Dock 2010 assessment. Structure. 2011 Aug 10;19(8):1108-26. doi:
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172: Svobodová Vareková R, Geidl S, Ionescu CM, Skrehota O, Kudera M, Sehnal D,
Bouchal T, Abagyan R, Huber HJ, Koca J. 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.
doi: 10.1021/ci200133w. Epub 2011 Aug 1. PMID: 21761919.
173: Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K,
Teplov A, Burley SK, Darnell RB, Patel DJ. 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. doi: 10.1016/j.str.2011.05.002. PMID:
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174: 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.
Structure of the human histamine H1 receptor complex with doxepin. Nature. 2011
Jun 22;475(7354):65-70. doi: 10.1038/nature10236. PMID: 21697825; PMCID:
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175: Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A. Systematic
exploitation of multiple receptor conformations for virtual ligand screening.
PLoS One. 2011;6(5):e18845. doi: 10.1371/journal.pone.0018845. Epub 2011 May 17.
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176: Dong M, Lam PC, Pinon DI, Hosohata K, Orry A, Sexton PM, Abagyan R, Miller
LJ. Molecular basis of secretin docking to its intact receptor using multiple
photolabile probes distributed throughout the pharmacophore. J Biol Chem. 2011
Jul 8;286(27):23888-99. doi: 10.1074/jbc.M111.245969. Epub 2011 May 12. PMID:
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177: Lee WH, Yue WW, Raush E, Totrov M, Abagyan R, Oppermann U, Marsden BD.
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. doi:
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178: Miller LJ, Chen Q, Lam PC, Pinon DI, Sexton PM, Abagyan R, Dong M.
Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-
region photolabile probes and molecular modeling. J Biol Chem. 2011 May
6;286(18):15895-907. doi: 10.1074/jbc.M110.217901. Epub 2011 Mar 16. PMID:
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179: Dey R, Chen L. In search of allosteric modulators of a7-nAChR by solvent
density guided virtual screening. J Biomol Struct Dyn. 2011 Apr;28(5):695-715.
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180: Leung CH, Chan DS, Yang H, Abagyan R, Lee SM, Zhu GY, Fong WF, Ma DL. A
natural product-like inhibitor of NEDD8-activating enzyme. Chem Commun (Camb).
2011 Mar 7;47(9):2511-3. doi: 10.1039/c0cc04927a. Epub 2011 Jan 14. PMID:
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181: Arnautova YA, Abagyan RA, Totrov M. 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. doi: 10.1002/prot.22896. PMID:
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182: 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. Structures
of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.
Science. 2010 Nov 19;330(6007):1066-71. doi: 10.1126/science.1194396. Epub 2010
Oct 7. PMID: 20929726; PMCID: PMC3074590.
183: Rueda M, Katritch V, Raush E, Abagyan R. SimiCon: a web tool for protein-
ligand model comparison through calculation of equivalent atomic contacts.
Bioinformatics. 2010 Nov 1;26(21):2784-5. doi: 10.1093/bioinformatics/btq504.
Epub 2010 Sep 24. PMID: 20871105; PMCID: PMC2981495.
184: Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, Stevens
RC. 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. doi: 10.1021/ja105108q. PMID: 20669948; PMCID: PMC2923663.
185: 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. 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. doi: 10.1016/j.virol.2010.06.027. Epub 2010 Jul 21. Erratum
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186: Katritch V, Kufareva I, Abagyan R. Structure based prediction of subtype-
selectivity for adenosine receptor antagonists. Neuropharmacology. 2011
Jan;60(1):108-15. doi: 10.1016/j.neuropharm.2010.07.009. Epub 2010 Jul 15. PMID:
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187: Odell LR, Howan D, Gordon CP, Robertson MJ, Chau N, Mariana A, Whiting AE,
Abagyan R, Daniel JA, Gorgani NN, Robinson PJ, McCluskey A. 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. doi: 10.1021/jm100442u. PMID:
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188: 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. 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. doi:
10.1016/j.chembiol.2010.03.006. PMID: 20534345; PMCID: PMC2884008.
189: Park SJ, Kufareva I, Abagyan R. 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. doi:
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190: Cheltsov AV, Aoyagi M, Aleshin A, Yu EC, Gilliland T, Zhai D, Bobkov AA,
Reed JC, Liddington RC, Abagyan R. Vaccinia virus virulence factor N1L is a
novel promising target for antiviral therapeutic intervention. J Med Chem. 2010
May 27;53(10):3899-906. doi: 10.1021/jm901446n. PMID: 20441222; PMCID:
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191: Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL.
Structure-based discovery of natural-product-like TNF-α inhibitors. Angew Chem
Int Ed Engl. 2010 Apr 6;49(16):2860-4. doi: 10.1002/anie.200907360. Epub 2010
Mar 16. PMID: 20235259; PMCID: PMC4162403.
192: Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. Spatial chemical distance
based on atomic property fields. J Comput Aided Mol Des. 2010 Mar;24(3):173-82.
doi: 10.1007/s10822-009-9316-x. Epub 2010 Mar 13. PMID: 20229197; PMCID:
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193: Dong M, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ. 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. doi:
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194: Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I,
Stevens RC, Abagyan R. Structure-based discovery of novel chemotypes for
adenosine A(2A) receptor antagonists. J Med Chem. 2010 Feb 25;53(4):1799-809.
doi: 10.1021/jm901647p. PMID: 20095623; PMCID: PMC2826142.
195: Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R. GPCR 3D homology models
for ligand screening: lessons learned from blind predictions of adenosine A2a
receptor complex. Proteins. 2010 Jan;78(1):197-211. doi: 10.1002/prot.22507.
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196: Rueda M, Bottegoni G, Abagyan R. Recipes for the selection of experimental
protein conformations for virtual screening. J Chem Inf Model. 2010
Jan;50(1):186-93. doi: 10.1021/ci9003943. PMID: 20000587; PMCID: PMC2811216.
197: Chow KH, Sun RW, Lam JB, Li CK, Xu A, Ma DL, Abagyan R, Wang Y, Che CM. A
gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-
catenin pathway. Cancer Res. 2010 Jan 1;70(1):329-37. doi:
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198: Wu P, Ma DL, Leung CH, Yan SC, Zhu N, Abagyan R, Che CM. Stabilization of
G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and
down-regulation of c-myc oncogene expression. Chemistry. 2009 Dec
7;15(47):13008-21. doi: 10.1002/chem.200901943. PMID: 19876976.
199: Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD. SGC--structural biology
and human health: a new approach to publishing structural biology results. PLoS
One. 2009 Oct 20;4(10):e7675. doi: 10.1371/journal.pone.0007675. PMID: 19847312;
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200: Raush E, Totrov M, Marsden BD, Abagyan R. A new method for publishing
three-dimensional content. PLoS One. 2009 Oct 20;4(10):e7394. doi:
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201: Abagyan R, Kufareva I. The flexible pocketome engine for structural
chemogenomics. Methods Mol Biol. 2009;575:249-79. doi:
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202: Bisson WH, Koch DC, O'Donnell EF, Khalil SM, Kerkvliet NI, Tanguay RL,
Abagyan R, Kolluri SK. 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. doi: 10.1021/jm900199u. PMID:
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203: Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J,
Chacon P. FRODOCK: a new approach for fast rotational protein-protein docking.
Bioinformatics. 2009 Oct 1;25(19):2544-51. doi: 10.1093/bioinformatics/btp447.
Epub 2009 Jul 20. PMID: 19620099; PMCID: PMC2800348.
204: Simms J, Hall NE, Lam PH, Miller LJ, Christopoulos A, Abagyan R, Sexton PM.
Homology modeling of GPCRs. Methods Mol Biol. 2009;552:97-113. doi:
10.1007/978-1-60327-317-6_7. PMID: 19513644.
205: Dong M, Lam PC, Pinon DI, Abagyan R, Miller LJ. 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. doi: 10.1021/bi9004705. PMID: 19441839; PMCID:
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206: Rueda M, Bottegoni G, Abagyan R. 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. doi: 10.1021/ci8003732. PMID:
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207: Gao F, Harikumar KG, Dong M, Lam PC, Sexton PM, Christopoulos A, Bordner A,
Abagyan R, Miller LJ. 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. doi: 10.1124/mol.109.055756. Epub 2009 May 8.
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208: Katritch V, Reynolds KA, Cherezov V, Hanson MA, Roth CB, Yeager M, Abagyan
R. 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. doi: 10.1002/jmr.949. PMID:
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209: Wu YW, Goody RS, Abagyan R, Alexandrov K. 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 8;284(19):13185-92. doi: 10.1074/jbc.M900579200. Epub 2009 Feb 24. PMID:
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210: Nicola G, Abagyan R. Structure-based approaches to antibiotic drug
discovery. Curr Protoc Microbiol. 2009 Feb;Chapter 17:Unit17.2. doi:
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211: Reynolds KA, Katritch V, Abagyan R. 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. doi: 10.1007/s10822-008-9257-9. Epub 2009 Jan 16. PMID:
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212: Bottegoni G, Kufareva I, Totrov M, Abagyan R. 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. doi: 10.1021/jm8009958. PMID: 19090659;
PMCID: PMC2662720.
213: Kufareva I, Abagyan R. 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. doi: 10.1021/jm8010299. PMID: 19053777; PMCID:
PMC2669721.
214: Bisson WH, Abagyan R, Cavasotto CN. 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. doi: 10.1016/j.jmgm.2008.08.001. Epub
2008 Aug 9. PMID: 18805032.
215: Kovacs JA, Yeager M, Abagyan R. Damped-dynamics flexible fitting. Biophys
J. 2008 Oct;95(7):3192-207. doi: 10.1529/biophysj.108.132357. Epub 2008 Jun 27.
PMID: 18586844; PMCID: PMC2547429.
216: Dong M, Lam PC, Pinon DI, Sexton PM, Abagyan R, Miller LJ. 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. doi: 10.1124/mol.108.047209. Epub
2008 May 8. PMID: 18467541; PMCID: PMC3879803.
217: Ma DL, Lai TS, Chan FY, Chung WH, Abagyan R, Leung YC, Wong KY. Discovery
of a drug-like G-quadruplex binding ligand by high-throughput docking.
ChemMedChem. 2008 Jun;3(6):881-4. doi: 10.1002/cmdc.200700342. PMID: 18383062.
218: Nicola G, Smith CA, Abagyan R. New method for the assessment of all drug-
like pockets across a structural genome. J Comput Biol. 2008 Apr;15(3):231-40.
doi: 10.1089/cmb.2007.0178. PMID: 18333758; PMCID: PMC2660599.
219: Totrov M, Abagyan R. Flexible ligand docking to multiple receptor
conformations: a practical alternative. Curr Opin Struct Biol. 2008
Apr;18(2):178-84. doi: 10.1016/j.sbi.2008.01.004. Epub 2008 Feb 25. PMID:
18302984; PMCID: PMC2396190.
220: Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S.
Optimization of high throughput virtual screening by combining shape-matching
and docking methods. J Chem Inf Model. 2008 Mar;48(3):489-97. doi:
10.1021/ci700376c. Epub 2008 Feb 27. PMID: 18302357.
221: Bottegoni G, Kufareva I, Totrov M, Abagyan R. 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. doi: 10.1007/s10822-008-9188-5.
Epub 2008 Feb 14. PMID: 18273556; PMCID: PMC2641994.
222: Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J. Docking analysis of
transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin
and flavodoxin. Proteins. 2008 Aug 15;72(3):848-62. doi: 10.1002/prot.21979.
PMID: 18260112; PMCID: PMC4162409.
223: 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 Jr.
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. doi: 10.1021/jm070759m. Epub 2008 Jan 17. PMID:
18198821.
224: Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva
I, Abagyan R, Broide DH, Lee J, Raz E. 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. doi: 10.1073/pnas.0709261104.
Epub 2007 Nov 14. PMID: 18003900; PMCID: PMC2141826.
225: Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan
R, Hruby DE. 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. doi: 10.1007/s10822-007-9138-7.
Epub 2007 Oct 25. PMID: 17960327; PMCID: PMC7087885.
226: Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B,
Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA. De novo discovery of
serotonin N-acetyltransferase inhibitors. J Med Chem. 2007 Nov 1;50(22):5330-8.
doi: 10.1021/jm0706463. Epub 2007 Oct 9. PMID: 17924613; PMCID: PMC2531295.
227: Mallya M, Phillips RL, Saldanha SA, Gooptu B, Brown SC, Termine DJ,
Shirvani AM, Wu Y, Sifers RN, Abagyan R, Lomas DA. Small molecules block the
polymerization of Z alpha1-antitrypsin and increase the clearance of
intracellular aggregates. J Med Chem. 2007 Nov 1;50(22):5357-63. doi:
10.1021/jm070687z. Epub 2007 Oct 5. PMID: 17918823; PMCID: PMC2631427.
228: Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H,
Pasquale EB, Kuhn P. 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. doi: 10.1074/jbc.M706340200. Epub 2007 Sep
26. PMID: 17897949; PMCID: PMC4370777.
229: Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ. 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 9;282(45):32834-43. doi:
10.1074/jbc.M704563200. Epub 2007 Sep 7. PMID: 17827151.
230: 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. Discovery of
antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc Natl
Acad Sci U S A. 2007 Jul 17;104(29):11927-32. doi: 10.1073/pnas.0609752104. Epub
2007 Jul 2. PMID: 17606915; PMCID: PMC1924583.
231: 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. Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity
in models of Parkinson's disease. Science. 2007 Jul 27;317(5837):516-9. doi:
10.1126/science.1143780. Epub 2007 Jun 21. PMID: 17588900.
232: Kovacs JA, Baker KA, Altenberg GA, Abagyan R, Yeager M. Molecular modeling
and mutagenesis of gap junction channels. Prog Biophys Mol Biol. 2007 May-
Jun;94(1-2):15-28. doi: 10.1016/j.pbiomolbio.2007.03.013. Epub 2007 Mar 23.
PMID: 17524457; PMCID: PMC2819402.
233: Nicola G, Smith CA, Lucumi E, Kuo MR, Karagyozov L, Fidock DA, Sacchettini
JC, Abagyan R. Discovery of novel inhibitors targeting enoyl-acyl carrier
protein reductase in Plasmodium falciparum by structure-based virtual screening.
Biochem Biophys Res Commun. 2007 Jul 6;358(3):686-91. doi:
10.1016/j.bbrc.2007.04.113. Epub 2007 Apr 26. PMID: 17509532; PMCID: PMC1987361.
234: Raduner S, Bisson W, Abagyan R, Altmann KH, Gertsch J. Self-assembling
cannabinomimetics: supramolecular structures of N-alkyl amides. J Nat Prod. 2007
Jun;70(6):1010-5. doi: 10.1021/np060598+. Epub 2007 May 11. PMID: 17497806.
235: Kovacs JA, Yeager M, Abagyan R. Computational prediction of atomic
structures of helical membrane proteins aided by EM maps. Biophys J. 2007 Sep
15;93(6):1950-9. doi: 10.1529/biophysj.106.102137. Epub 2007 May 11. PMID:
17496035; PMCID: PMC1959528.
236: Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller
LJ. 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. doi:
10.1124/mol.107.035402. Epub 2007 May 2. PMID: 17475809.
237: Dong M, Ding XQ, Thomas SE, Gao F, Lam PC, Abagyan R, Miller LJ. 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. doi: 10.1021/bi0622468. Epub 2007 Mar
24. PMID: 17381074; PMCID: PMC2580722.
238: Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. PIER: protein
interface recognition for structural proteomics. Proteins. 2007 May
1;67(2):400-17. doi: 10.1002/prot.21233. PMID: 17299750.
239: Garzón JI, Kovacs J, Abagyan R, Chacón P. DFprot: a webtool for predicting
local chain deformability. Bioinformatics. 2007 Apr 1;23(7):901-2. doi:
10.1093/bioinformatics/btm014. Epub 2007 Feb 3. PMID: 17277334.
240: Saldanha SA, Kaler G, Cottam HB, Abagyan R, Taylor SS. 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. doi: 10.1021/ac061104g. PMID: 17165815; PMCID: PMC3435108.
241: Garzón JI, Kovacs J, Abagyan R, Chacón P. ADP_EM: fast exhaustive multi-
resolution docking for high-throughput coverage. Bioinformatics. 2007 Feb
15;23(4):427-33. doi: 10.1093/bioinformatics/btl625. Epub 2006 Dec 6. PMID:
17150992.
242: Malinina L, Malakhova ML, Kanack AT, Lu M, Abagyan R, Brown RE, Patel DJ.
The liganding of glycolipid transfer protein is controlled by glycolipid acyl
structure. PLoS Biol. 2006 Nov;4(11):e362. doi: 10.1371/journal.pbio.0040362.
PMID: 17105344; PMCID: PMC1618416.
243: Budagyan L, Abagyan R. Weighted quality estimates in machine learning.
Bioinformatics. 2006 Nov 1;22(21):2597-603. doi: 10.1093/bioinformatics/btl458.
Epub 2006 Aug 25. PMID: 16935929.
244: Altmann SM, Muryshev A, Fossale E, Maxwell MM, Norflus FN, Fox J, Hersch
SM, Young AB, MacDonald ME, Abagyan R, Kazantsev AG. Discovery of bioactive
small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-
deficient cells. Chem Biol. 2006 Jul;13(7):765-70. doi:
10.1016/j.chembiol.2006.05.012. PMID: 16873024.
245: Huang Y, Qiao F, Abagyan R, Hazard S, Tomlinson S. Defining the CD59-C9
binding interaction. J Biol Chem. 2006 Sep 15;281(37):27398-404. doi:
10.1074/jbc.M603690200. Epub 2006 Jul 14. PMID: 16844690.
246: Orry AJ, Abagyan RA, Cavasotto CN. Structure-based development of target-
specific compound libraries. Drug Discov Today. 2006 Mar;11(5-6):261-6. doi:
10.1016/S1359-6446(05)03717-7. PMID: 16580603.
247: Bordner AJ, Abagyan R. Ab initio prediction of peptide-MHC binding geometry
for diverse class I MHC allotypes. Proteins. 2006 May 15;63(3):512-26. doi:
10.1002/prot.20831. PMID: 16470819.
248: Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G. XCMS: processing mass
spectrometry data for metabolite profiling using nonlinear peak alignment,
matching, and identification. Anal Chem. 2006 Feb 1;78(3):779-87. doi:
10.1021/ac051437y. PMID: 16448051.
249: Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ. In silico identification
of novel EGFR inhibitors with antiproliferative activity against cancer cells.
Bioorg Med Chem Lett. 2006 Apr 1;16(7):1969-74. doi: 10.1016/j.bmcl.2005.12.067.
Epub 2006 Jan 18. PMID: 16413185.
250: Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, Marsden BD.
Disseminating structural genomics data to the public: from a data dump to an
animated story. Trends Biochem Sci. 2006 Feb;31(2):76-8. doi:
10.1016/j.tibs.2005.12.006. Epub 2006 Jan 6. PMID: 16406633.
251: Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE,
Abagyan R, Siuzdak G. METLIN: a metabolite mass spectral database. Ther Drug
Monit. 2005 Dec;27(6):747-51. doi: 10.1097/01.ftd.0000179845.53213.39. PMID:
16404815.
252: Cardozo T, Abagyan R. Druggability of SCF ubiquitin ligase-protein
interfaces. Methods Enzymol. 2005;399:634-53. doi:
10.1016/S0076-6879(05)99042-3. PMID: 16338386.
253: Hill T, Odell LR, Edwards JK, Graham ME, McGeachie AB, Rusak J, Quan A,
Abagyan R, Scott JL, Robinson PJ, McCluskey A. Small molecule inhibitors of
dynamin I GTPase activity: development of dimeric tyrphostins. J Med Chem. 2005
Dec 1;48(24):7781-8. doi: 10.1021/jm040208l. PMID: 16302817.
254: Tetko IV, Abagyan R, Oprea TI. Surrogate data--a secure way to share
corporate data. J Comput Aided Mol Des. 2005 Sep-Oct;19(9-10):749-64. doi:
10.1007/s10822-005-9013-3. Epub 2005 Nov 3. PMID: 16267691.
255: Huang Y, Smith CA, Song H, Morgan BP, Abagyan R, Tomlinson S. Insights into
the human CD59 complement binding interface toward engineering new therapeutics.
J Biol Chem. 2005 Oct 7;280(40):34073-9. doi: 10.1074/jbc.M504922200. Epub 2005
Aug 3. PMID: 16079145.
256: Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in
ligand docking through relevant normal modes. J Am Chem Soc. 2005 Jul
6;127(26):9632-40. doi: 10.1021/ja042260c. PMID: 15984891.
257: 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. Efficient synthetic inhibitors of anthrax lethal
factor. Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9499-504. doi:
10.1073/pnas.0502733102. Epub 2005 Jun 27. PMID: 15983377; PMCID: PMC1160517.
258: Fernández-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions:
optimized desolvation for rigid-body docking. Proteins. 2005 Aug 1;60(2):308-13.
doi: 10.1002/prot.20575. PMID: 15981266.
259: Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-
protein interfaces. Proteins. 2005 Aug 15;60(3):353-66. doi: 10.1002/prot.20433.
PMID: 15906321.
260: An J, Totrov M, Abagyan R. Pocketome via comprehensive identification and
classification of ligand binding envelopes. Mol Cell Proteomics. 2005
Jun;4(6):752-61. doi: 10.1074/mcp.M400159-MCP200. Epub 2005 Mar 9. PMID:
15757999.
261: Bordner AJ, Abagyan R. REVCOM: a robust Bayesian method for evolutionary
rate estimation. Bioinformatics. 2005 May 15;21(10):2315-21. doi:
10.1093/bioinformatics/bti347. Epub 2005 Mar 4. PMID: 15749694.
262: An J, Totrov M, Abagyan R. Comprehensive identification of "druggable"
protein ligand binding sites. Genome Inform. 2004;15(2):31-41. PMID: 15706489.
263: Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area:
a new method for predicting protein-protein interaction sites. Proteins. 2005
Jan 1;58(1):134-43. doi: 10.1002/prot.20285. PMID: 15495260.
264: Bordner AJ, Abagyan RA. Large-scale prediction of protein geometry and
stability changes for arbitrary single point mutations. Proteins. 2004 Nov
1;57(2):400-13. doi: 10.1002/prot.20185. PMID: 15340927.
265: Cavasotto CN, Liu G, James SY, Hobbs PD, Peterson VJ, Bhattacharya AA,
Kolluri SK, Zhang XK, Leid M, Abagyan R, Liddington RC, Dawson MI. Determinants
of retinoid X receptor transcriptional antagonism. J Med Chem. 2004 Aug
26;47(18):4360-72. doi: 10.1021/jm030651g. PMID: 15317450.
266: Kovacs JA, Chacón P, Abagyan R. Predictions of protein flexibility: first-
order measures. Proteins. 2004 Sep 1;56(4):661-8. doi: 10.1002/prot.20151. PMID:
15281119.
267: Hill TA, Odell LR, Quan A, Abagyan R, Ferguson G, Robinson PJ, McCluskey A.
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. doi:
10.1016/j.bmcl.2004.03.096. PMID: 15149689.
268: Marsden B, Abagyan R. SAD--a normalized structural alignment database:
improving sequence-structure alignments. Bioinformatics. 2004 Oct
12;20(15):2333-44. doi: 10.1093/bioinformatics/bth244. Epub 2004 Apr 15. PMID:
15087320.
269: Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd. Comparative study of
several algorithms for flexible ligand docking. J Comput Aided Mol Des. 2003
Nov;17(11):755-63. doi: 10.1023/b:jcam.0000017496.76572.6f. PMID: 15072435.
270: Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual
screening to protein kinases. J Mol Biol. 2004 Mar 12;337(1):209-25. doi:
10.1016/j.jmb.2004.01.003. PMID: 15001363.
271: Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein
interaction sites from docking energy landscapes. J Mol Biol. 2004 Jan
16;335(3):843-65. doi: 10.1016/j.jmb.2003.10.069. PMID: 14687579.
272: Zhou Y, Abagyan R. Algorithms for high-density oligonucleotide array. Curr
Opin Drug Discov Devel. 2003 May;6(3):339-45. PMID: 12833666.
273: Schapira M, Abagyan R, Totrov M. Nuclear hormone receptor targeted virtual
screening. J Med Chem. 2003 Jul 3;46(14):3045-59. doi: 10.1021/jm0300173. PMID:
12825943.
274: Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy
optimization with fully flexible side-chains. Proteins. 2003 Jul 1;52(1):113-7.
doi: 10.1002/prot.10383. PMID: 12784376.
275: Schapira M, Raaka BM, Das S, Fan L, Totrov M, Zhou Z, Wilson SR, Abagyan R,
Samuels HH. 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. doi:
10.1073/pnas.1131854100. Epub 2003 May 30. PMID: 12777627; PMCID: PMC165879.
276: Cavasotto CN, Orry AJ, Abagyan RA. Structure-based identification of
binding sites, native ligands and potential inhibitors for G-protein coupled
receptors. Proteins. 2003 May 15;51(3):423-33. doi: 10.1002/prot.10362. PMID:
12696053.
277: Eneqvist T, Lundberg E, Nilsson L, Abagyan R, Sauer-Eriksson AE. The
transthyretin-related protein family. Eur J Biochem. 2003 Feb;270(3):518-32.
doi: 10.1046/j.1432-1033.2003.03408.x. PMID: 12542701.
278: Katritch V, Totrov M, Abagyan R. ICFF: a new method to incorporate implicit
flexibility into an internal coordinate force field. J Comput Chem. 2003 Jan
30;24(2):254-65. doi: 10.1002/jcc.10091. PMID: 12497604.
279: Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y,
Plouffe D, Le Roch KG, Abagyan R, Winzeler EA. Excess polymorphisms in genes for
membrane proteins in Plasmodium falciparum. Science. 2002 Oct 4;298(5591):216-8.
doi: 10.1126/science.1075642. PMID: 12364807.
280: Brive L, Abagyan R. Computational structural proteomics. Ernst Schering Res
Found Workshop. 2002;(38):149-66. doi: 10.1007/978-3-662-04747-7_8. PMID:
12061000.
281: Fernandez-Recio J, Totrov M, Abagyan R. Screened charge electrostatic model
in protein-protein docking simulations. Pac Symp Biocomput. 2002:552-63. PMID:
11928507.
282: Schapira M, Abagyan R, Totrov M. Structural model of nicotinic
acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct
Biol. 2002;2:1. doi: 10.1186/1472-6807-2-1. Epub 2002 Jan 18. PMID: 11860617;
PMCID: PMC65631.
283: Zhou Y, Abagyan R. Match-only integral distribution (MOID) algorithm for
high-density oligonucleotide array analysis. BMC Bioinformatics. 2002;3:3. doi:
10.1186/1471-2105-3-3. Epub 2002 Jan 22. PMID: 11835687; PMCID: PMC65509.
284: Fernández-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in
internal coordinates. Protein Sci. 2002 Feb;11(2):280-91. doi: 10.1110/ps.19202.
PMID: 11790838; PMCID: PMC2373434.
285: Abagyan R, Totrov M. High-throughput docking for lead generation. Curr Opin
Chem Biol. 2001 Aug;5(4):375-82. doi: 10.1016/s1367-5931(00)00217-9. PMID:
11470599.
286: Totrov M, Abagyan R. Rapid boundary element solvation electrostatics
calculations in folding simulations: successful folding of a 23-residue peptide.
Biopolymers. 2001;60(2):124-33. doi: 10.1002/1097-0282(2001)60:2<124::AID-
BIP1008>3.0.CO;2-S. PMID: 11455546.
287: Schapira M, Raaka BM, Samuels HH, Abagyan R. In silico discovery of novel
retinoic acid receptor agonist structures. BMC Struct Biol. 2001;1:1. doi:
10.1186/1472-6807-1-1. Epub 2001 Jun 4. PMID: 11405897; PMCID: PMC32304.
288: Norledge BV, Lambeir AM, Abagyan RA, Rottmann A, Fernandez AM, Filimonov
VV, Peter MG, Wierenga RK. 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. doi:
10.1002/1097-0134(20010215)42:3<383::aid-prot80>3.0.co;2-g. PMID: 11151009.
289: Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL.
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. doi:
10.1023/a:1008121029716. PMID: 10921774.
290: Gantt S, Persson C, Rose K, Birkett AJ, Abagyan R, Nussenzweig V.
Antibodies against thrombospondin-related anonymous protein do not inhibit
Plasmodium sporozoite infectivity in vivo. Infect Immun. 2000 Jun;68(6):3667-73.
doi: 10.1128/IAI.68.6.3667-3673.2000. PMID: 10816526; PMCID: PMC97657.
291: 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.
Genetic linkage mapping of zebrafish genes and ESTs. Genome Res. 2000
Apr;10(4):558-67. doi: 10.1101/gr.10.4.558. PMID: 10779498; PMCID: PMC310859.
292: Jin E, Katritch V, Olson WK, Kharatisvili M, Abagyan R, Pilch DS.
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. doi: 10.1006/jmbi.2000.3639. PMID: 10756107.
293: Tomko RP, Johansson CB, Totrov M, Abagyan R, Frisén J, Philipson L.
Expression of the adenovirus receptor and its interaction with the fiber knob.
Exp Cell Res. 2000 Feb 25;255(1):47-55. doi: 10.1006/excr.1999.4761. PMID:
10666333.
294: Schapira M, Raaka BM, Samuels HH, Abagyan R. Rational discovery of novel
nuclear hormone receptor antagonists. Proc Natl Acad Sci U S A. 2000 Feb
1;97(3):1008-13. doi: 10.1073/pnas.97.3.1008. PMID: 10655475; PMCID: PMC15503.
295: Cardozo T, Batalov S, Abagyan R. Estimating local backbone structural
deviation in homology models. Comput Chem. 2000 Jan;24(1):13-31. doi:
10.1016/s0097-8485(99)00044-3. PMID: 10642877.
296: Li D, Desai-Yajnik V, Lo E, Schapira M, Abagyan R, Samuels HH. NRIF3 is a
novel coactivator mediating functional specificity of nuclear hormone receptors.
Mol Cell Biol. 1999 Oct;19(10):7191-202. doi: 10.1128/MCB.19.10.7191. PMID:
10490654; PMCID: PMC84712.
297: Stigler RD, Hoffmann B, Abagyan R, Schneider-Mergener J. 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. doi:
10.1016/s0969-2126(99)80087-2. PMID: 10404595.
298: Schapira M, Totrov M, Abagyan R. Prediction of the binding energy for small
molecules, peptides and proteins. J Mol Recognit. 1999 May-Jun;12(3):177-90.
doi: 10.1002/(SICI)1099-1352(199905/06)12:3<177::AID-JMR451>3.0.CO;2-Z. PMID:
10398408.
299: Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D,
Abagyan R, Schier AF, Talbot WS. A genetic linkage map for zebrafish:
comparative analysis and localization of genes and expressed sequences. Genome
Res. 1999 Apr;9(4):334-47. PMID: 10207156.
300: Zhang HF, Yu J, Chen S, Morgan BP, Abagyan R, Tomlinson S. Identification
of the individual residues that determine human CD59 species selective activity.
J Biol Chem. 1999 Apr 16;274(16):10969-74. doi: 10.1074/jbc.274.16.10969. PMID:
10196177.
301: Zhou Y, Abagyan R. How and why phosphotyrosine-containing peptides bind to
the SH2 and PTB domains. Fold Des. 1998;3(6):513-22. doi:
10.1016/S1359-0278(98)00067-4. PMID: 9889165.
302: Srivastava S, Osten P, Vilim FS, Khatri L, Inman G, States B, Daly C,
DeSouza S, Abagyan R, Valtschanoff JG, Weinberg RJ, Ziff EB. Novel anchorage of
GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP.
Neuron. 1998 Sep;21(3):581-91. doi: 10.1016/s0896-6273(00)80568-1. PMID:
9768844.
303: Isakoff SJ, Cardozo T, Andreev J, Li Z, Ferguson KM, Abagyan R, Lemmon MA,
Aronheim A, Skolnik EY. 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. doi: 10.1093/emboj/17.18.5374. PMID:
9736615; PMCID: PMC1170863.
304: Maiorov V, Abagyan R. Energy strain in three-dimensional protein
structures. Fold Des. 1998;3(4):259-69. doi: 10.1016/S1359-0278(98)00037-6.
PMID: 9710569.
305: Patel IR, Attur MG, Patel RN, Stuchin SA, Abagyan RA, Abramson SB, Amin AR.
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 1;160(9):4570-9. PMID: 9574564.
306: Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen
B, Lamzin VS, Kunau WH, Wierenga RK. 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. doi: 10.1006/jmbi.1997.1331. PMID: 9402066.
307: Abagyan RA, Batalov S. Do aligned sequences share the same fold? J Mol
Biol. 1997 Oct 17;273(1):355-68. doi: 10.1006/jmbi.1997.1287. PMID: 9367768.
308: Rashin AA, Rashin BH, Rashin A, Abagyan R. Evaluating the energetics of
empty cavities and internal mutations in proteins. Protein Sci. 1997
Oct;6(10):2143-58. doi: 10.1002/pro.5560061009. PMID: 9336837; PMCID:
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309: Yu J, Dong S, Rushmere NK, Morgan BP, Abagyan R, Tomlinson S. Mapping the
regions of the complement inhibitor CD59 responsible for its species selective
activity. Biochemistry. 1997 Aug 5;36(31):9423-8. doi: 10.1021/bi970832i. PMID:
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310: Koonin EV, Abagyan RA. TSG101 may be the prototype of a class of dominant
negative ubiquitin regulators. Nat Genet. 1997 Aug;16(4):330-1. doi:
10.1038/ng0897-330. PMID: 9241264.
311: Abagyan RA, Totrov MM. Contact area difference (CAD): a robust measure to
evaluate accuracy of protein models. J Mol Biol. 1997 May 9;268(3):678-85. doi:
10.1006/jmbi.1997.0994. PMID: 9171291.
312: Maiorov V, Abagyan R. A new method for modeling large-scale rearrangements
of protein domains. Proteins. 1997 Mar;27(3):410-24. doi:
10.1002/(sici)1097-0134(199703)27:3<410::aid-prot9>3.0.co;2-g. PMID: 9094743.
313: Yu J, Abagyan R, Dong S, Gilbert A, Nussenzweig V, Tomlinson S. Mapping the
active site of CD59. J Exp Med. 1997 Feb 17;185(4):745-53. doi:
10.1084/jem.185.4.745. PMID: 9034152; PMCID: PMC2196154.
314: Thanki N, Zeelen JP, Mathieu M, Jaenicke R, Abagyan RA, Wierenga RK,
Schliebs W. 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. doi: 10.1093/protein/10.2.159. PMID:
9089815.
315: Totrov M, Abagyan R. Flexible protein-ligand docking by global energy
optimization in internal coordinates. Proteins. 1997;Suppl 1:215-20. doi:
10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.3.co;2-i. PMID: 9485515.
316: Abagyan R, Batalov S, Cardozo T, Totrov M, Webber J, Zhou Y. Homology
modeling with internal coordinate mechanics: deformation zone mapping and
improvements of models via conformational search. Proteins. 1997;Suppl 1:29-37.
doi: 10.1002/(sici)1097-0134(1997)1+<29::aid-prot5>3.3.co;2-4. PMID: 9485492.
317: Goodman AR, Cardozo T, Abagyan R, Altmeyer A, Wisniewski HG, Vilcek J. Long
pentraxins: an emerging group of proteins with diverse functions. Cytokine
Growth Factor Rev. 1996 Aug;7(2):191-202. doi: 10.1016/1359-6101(96)00019-6.
PMID: 8899296.
318: Chalikian TV, Totrov M, Abagyan R, Breslauer KJ. 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. doi: 10.1006/jmbi.1996.0423. PMID: 8759322.
319: 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. 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. doi: 10.1038/nsb0396-233. PMID:
8605624.
320: Totrov M, Abagyan R. The contour-buildup algorithm to calculate the
analytical molecular surface. J Struct Biol. 1996 Jan-Feb;116(1):138-43. doi:
10.1006/jsbi.1996.0022. PMID: 8742735.
321: Cardozo T, Totrov M, Abagyan R. Homology modeling by the ICM method.
Proteins. 1995 Nov;23(3):403-14. doi: 10.1002/prot.340230314. PMID: 8710833.
322: Borchert TV, Kishan KV, Zeelen JP, Schliebs W, Thanki N, Abagyan R,
Jaenicke R, Wierenga RK. 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. doi: 10.1016/s0969-2126(01)00202-7. PMID: 8591044.
323: Houbrechts A, Moreau B, Abagyan R, Mainfroid V, Préaux G, Lamproye A,
Poncin A, Goormaghtigh E, Ruysschaert JM, Martial JA, et al. 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. doi:
10.1093/protein/8.3.249. PMID: 7479687.
324: Argos P, Abagyan R. The protein folding problem: finding a few minimums in
a near infinite space. Comput Chem. 1994 Sep;18(3):225-31. doi:
10.1016/0097-8485(94)85017-8. PMID: 7952893.
325: Abagyan R, Frishman D, Argos P. Recognition of distantly related proteins
through energy calculations. Proteins. 1994 Jun;19(2):132-40. doi:
10.1002/prot.340190206. PMID: 8090707.
326: Totrov M, Abagyan R. Detailed ab initio prediction of lysozyme-antibody
complex with 1.6 A accuracy. Nat Struct Biol. 1994 Apr;1(4):259-63. doi:
10.1038/nsb0494-259. PMID: 7656055.
327: Borchert TV, Abagyan R, Jaenicke R, Wierenga RK. Design, creation, and
characterization of a stable, monomeric triosephosphate isomerase. Proc Natl
Acad Sci U S A. 1994 Feb 15;91(4):1515-8. doi: 10.1073/pnas.91.4.1515. PMID:
8108439; PMCID: PMC43190.
328: Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches
and electrostatic calculations for peptides and proteins. J Mol Biol. 1994 Jan
21;235(3):983-1002. doi: 10.1006/jmbi.1994.1052. PMID: 8289329.
329: Kuznetsov DA, Abagyan RA. A technique for identifying atoms from a screen
image. J Mol Graph. 1993 Dec;11(4):245-7. doi: 10.1016/0263-7855(93)80004-b.
PMID: 8136327.
330: Borchert TV, Abagyan R, Kishan KV, Zeelen JP, Wierenga RK. 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.
doi: 10.1016/0969-2126(93)90021-8. PMID: 16100954.
331: Dorofeyev VE, Mazur AK. Investigation of conformational equilibrium of
polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin. J
Biomol Struct Dyn. 1993 Aug;11(1):143-67. doi: 10.1080/07391102.1993.10508714.
PMID: 8216941.
332: Abagyan RA. Towards protein folding by global energy optimization. FEBS
Lett. 1993 Jun 28;325(1-2):17-22. doi: 10.1016/0014-5793(93)81406-p. PMID:
8513887.
333: Eisenmenger F, Argos P, Abagyan R. A method to configure protein side-
chains from the main-chain trace in homology modelling. J Mol Biol. 1993 Jun
5;231(3):849-60. doi: 10.1006/jmbi.1993.1331. PMID: 8515455.
334: Gibson TJ, Thompson JD, Abagyan RA. 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. doi: 10.1093/protein/6.1.41. PMID: 8433970.
335: Abagyan R, Argos P. Optimal protocol and trajectory visualization for
conformational searches of peptides and proteins. J Mol Biol. 1992 May
20;225(2):519-32. doi: 10.1016/0022-2836(92)90936-e. PMID: 1593634.
336: Abagyan RA, Mironov VN, Chernov BK, Chuprina VP, Ulyanov AV.
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. doi: 10.1093/nar/18.4.989. PMID: 2315048; PMCID: PMC330354.
337: Gromova II, Buchman VL, Abagyan RA, Ulyanov AV, Bronstein IB. 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.
doi: 10.1093/nar/18.3.637. PMID: 2155407; PMCID: PMC333473.
338: Eisenhaber F, Tumanyan VG, Abagyan RA. 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. doi:
10.1002/bip.360300509. PMID: 2265229.
339: Abagyan RA, Maiorov VN. 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. doi: 10.1080/07391102.1989.10506535. PMID:
2818856.
340: Abagyan RA, Mazur AK. 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. doi: 10.1080/07391102.1989.10507740. PMID:
2619943.
341: Mazur AK, Abagyan RA. 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. doi: 10.1080/07391102.1989.10507739. PMID: 2619942.
342: Chuprina VP, Abagyan RA. Structural basis of stable bending in DNA
containing An tracts. Different types of bending. J Biomol Struct Dyn. 1988
Aug;6(1):121-38. doi: 10.1080/07391102.1988.10506486. PMID: 3271514.
343: Abagyan RA, Maiorov VN. A simple qualitative representation of polypeptide
chain folds: comparison of protein tertiary structures. J Biomol Struct Dyn.
1988 Jun;5(6):1267-79. doi: 10.1080/07391102.1988.10506469. PMID: 3271511.
344: Chuprina VP, Abagyan RA. Anomalous properties of adenine.thymine tracts.
Nature. 1988 Mar 10;332(6160):117. doi: 10.1038/332117a0. PMID: 3347251.
345: Ivanitskiĭ GR, Esipova NG, Abagyan RA, Shnol' SE. Blochnoe
sovershenstvovanie geneticheskogo teksta kak faktor uskoreniia biologicheskoĭ
évoliutsii [Block improvement of the genetic text as a factor of acceleration of
biological evolution]. Biofizika. 1985 May-Jun;30(3):418-21. Russian. PMID:
4027270.
346: Abagyan RA, Tumanian VG, Esipova NG. Dva konformatsionnykh tipa tripeptidov
v kollagene. Raschet struktury politripeptidov (Gly-Pro-Ser)n i (Gly-Val-Hyp)n
[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. Russian. PMID: 6548632.
347: Abagyan RA. Skhema molekuliarnoĭ upakovki kollagena v fibrillakh
[Arrangement of molecular packing of collagen in fibrils]. Biofizika. 1983 May-
Jun;28(3):498-500. Russian. PMID: 6871272.
348: Abagyan RA. Difraktsiia ot znakoperemennoĭ spirali [Diffraction from the
alternating helix]. Biofizika. 1983 May-Jun;28(3):388-92. Russian. PMID:
6871260.
349: Rogulenkova VN, Abagyan RA, Tumanian VG, Esipova NG. Difraktsionnye éffekty
na rentgenogrammakh oligotripeptida (Gli-Pro-Pro)10, izomorfnogo kollagenu
[Diffraction effects on x-rays of the oligotripeptide (Gly-Pro-Pro)10,
isomorphic to collagen]. Biofizika. 1981 Jul-Aug;26(4):734-6. Russian. PMID:
7284464.
- Makunts T, Joulfayan H, Abagyan R. 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 1;5 .doi: 10.2196/55976. PMID: 38738836.
- Munson BP, Chen M, Bogosian A, Kreisberg JF, Licon K, Abagyan R, Kuenzi BM, Ideker T. De novo generation of multi-target compounds using deep generative chemistry. Nat Commun. 2024 May 6;15(1):3636. doi: 10.1038/s41467-024-47120-y. PMID: 38710699; PMCID: PMC11074339.
- Raush E, Abagyan R, Totrov M. 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. doi:10.1021/acs.jctc.4c00280. Epub 2024 Apr 26. PMID: 38669307.
- Makunts T, Grabska S, Grabski H, Abagyan R. Co-occurring infections in cancer patients treated with checkpoint inhibitors significantly increase the risk of immune related adverse events. medRxiv [Preprint]. 2024 Feb 15:2024.02.14.24302840. doi: 10.1101/2024.02.14.24302840. PMID: 38405974; PMCID: PMC10889010.
- 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. Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins. Cell Genom. 2023 May 30;3(7):100339. doi: 10.1016/j.xgen.2023.100339. PMID: 37492105; PMCID: PMC10363808.
- Joulfayan H, Makunts T, Abagyan R. Anti-TNF-α therapy induced psoriasis in rheumatoid arthritis patients according to FDA postmarketing surveillance data. Sci Rep. 2023 Jun 27;13(1):10448. doi: 10.1038/s41598-023-37010-6. PMID: 37369753; PMCID: PMC10300095.
- Makunts T, Dahill D, Jerome L, de Boer A, Abagyan R. Concomitant medications associated with ischemic, hypertensive, and arrhythmic events in MDMA users in FDA adverse event reporting system. Front Psychiatry. 2023 May 18;14:1149766. doi: 10.3389/fpsyt.2023.1149766. PMID: 37275981; PMCID: PMC10233020.
- Meewan I, Shiryaev SA, Kattoula J, Huang CT, Lin V, Chuang CH, Terskikh AV, Abagyan R. Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in "Super-Open" Conformation. Viruses. 2023 Apr 30;15(5):1106. doi: 10.3390/v15051106. PMID: 37243192; PMCID: PMC10224173.
- Sauvey C, Meewan I, Ehrenkaufer G, Blevitt J, Jackson P, Abagyan R. High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds. PLoS One. 2023 May 9;18(5):e0280232. doi: 10.1371/journal.pone.0280232. PMID: 37159460; PMCID: PMC10168566.
- Raush E, Abagyan R, Totrov M. 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. doi: 10.1021/acs.jcim.2c00790. Epub 2022 Dec 1. PMID: 36456533.
- Awdishu L, Abagyan R. Do Proton-Pump Inhibitors Cause CKD and Progression of CKD?: PRO. Kidney360. 2022 Jan 4;3(7):1134-1136. doi: 10.34067/KID.0007622021. PMID: 35919519; PMCID: PMC9337907.
- 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. Discovery of Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L. Pharmaceuticals (Basel). 2022 Jun 13;15(6):744. doi: 10.3390/ph15060744. PMID: 35745663; PMCID: PMC9230533.
- Bartholow TG, Sztain T, Young MA, Lee DJ, Davis TD, Abagyan R, Burkart MD. Control of Unsaturation in De Novo Fatty Acid Biosynthesis by FabA. Biochemistry. 2022 Apr 5;61(7):608-615. doi: 10.1021/acs.biochem.2c00094. PMID: 35255690; PMCID: PMC9769579.
- Rosenthal SB, Wang H, Shi D, Liu C, Abagyan R, McEvoy LK, Chen CH. Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics. PLoS Comput Biol. 2022 Feb 25;18(2):e1009903. doi: 10.1371/journal.pcbi.1009903. PMID: 35213535; PMCID: PMC8906581.
- Makunts T, Burkhart K, Abagyan R, Lee P. Retrospective analysis of clinical trial safety data for pembrolizumab reveals the effect of co-occurring infections on immune-related adverse events. PLoS One. 2022 Feb 10;17(2):e0263402. doi: 10.1371/journal.pone.0263402. PMID: 35143542; PMCID: PMC8830697.
- Makunts T, Jerome L, Abagyan R, de Boer A. Reported Cases of Serotonin Syndrome in MDMA Users in FAERS Database. Front Psychiatry. 2022 Jan 24;12:824288. doi: 10.3389/fpsyt.2021.824288. PMID: 35140642; PMCID: PMC8820588.
- 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. ARN25068, a versatile starting point towards triple GSK-3β/FYN/DYRK1A inhibitors to tackle tau-related neurological disorders. Eur J Med Chem. 2022 Feb 5;229:114054. doi: 10.1016/j.ejmech.2021.114054. Epub 2021 Dec 16. PMID: 34959172; PMCID: PMC9704499.
- Wollmer MA, Makunts T, Krüger THC, Abagyan R. Postmarketing safety surveillance data reveals protective effects of botulinum toxin injections against incident anxiety. Sci Rep. 2021 Dec 21;11(1):24173. doi: 10.1038/s41598-021-03713-x. PMID: 34934096; PMCID: PMC8692576.
- Keshishi D, Makunts T, Abagyan R. Common osteoporosis drug associated with increased rates of depression and anxiety. Sci Rep. 2021 Dec 14;11(1):23956. doi: 10.1038/s41598-021-03214-x. PMID: 34907232; PMCID: PMC8671447.
- Bartholow TG, Sztain T, Young MA, Davis TD, Abagyan R, Burkart MD. Protein-protein interaction based substrate control in the E. coli octanoic acid transferase, LipB. RSC Chem Biol. 2021 Jul 28;2(5):1466-1473. doi: 10.1039/d1cb00125f. PMID: 34704050; PMCID: PMC8495967.
- Nigam AK, Ojha AA, Li JG, Shi D, Bhatnagar V, Nigam KB, Abagyan R. 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):1720. doi:10.3390/pharmaceutics13101720. PMID: 34684013; PMCID: PMC8538396
- 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. Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.* PLoS Comput Biol.* 2021 Sep 14;17(9):e1009302. doi: 10.1371/journal.pcbi.1009302. PMID: 34520464; PMCID: PMC8483411.
- Makunts T, Saunders IM, Cohen IV, Li M, Moumedjian T, Issa MA, Burkhart K, Lee P, Patel SP, Abagyan R. Myocarditis occurrence with cancer immunotherapy across indications in clinical trial and post-marketing data. Sci Rep. 2021 Aug 30;11(1):17324. doi: 10.1038/s41598-021-96467-5. PMID: 34462476; PMCID: PMC8405813.
- Bartholow TG, Sztain T, Patel A, Lee DJ, Young MA, Abagyan R, Burkart MD. Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis. Commun Biol. 2021 Mar 16;4(1):340. doi: 10.1038/s42003-021-01838-3. PMID: 33727677; PMCID: PMC7966745.
- Cohen IV, Makunts T, Abagyan R, Thomas K. Concomitant drugs associated with increased mortality for MDMA users reported in a drug safety surveillance database. Sci Rep. 2021 Mar 16;11(1):5997. doi: 10.1038/s41598-021-85389-x. PMID: 33727616; PMCID: PMC7966744.
- Natala SR, Habas A, Stocking EM, Orry A, Price DL, Gill MB, Bonhaus DW, Abagyan R, Wrasidlo W. Structure based design and synthesis of novel Toll-like Receptor 2 (TLR 2) lipid antagonists. Bioorg Med Chem Lett. 2021 May 15;40:127861. doi: 10.1016/j.bmcl.2021.127861. Epub 2021 Feb 23. PMID: 33636302.
- Sauvey C, Ehrenkaufer G, Shi D, Debnath A, Abagyan R. Antineoplastic kinase inhibitors: A new class of potent anti-amoebic compounds. PLoS Negl Trop Dis. 2021 Feb 8;15(2):e0008425. doi: 10.1371/journal.pntd.0008425. PMID: 33556060; PMCID: PMC7895358.
- Nguyen VN, Abagyan R, Tsunoda SM. Mtor inhibitors associated with higher cardiovascular adverse events-A large population database analysis. Clin Transplant. 2021 Apr;35(4):e14228. doi: 10.1111/ctr.14228. Epub 2021 Feb 2. PMID: 33476406.
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