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    Ruben Abagyan

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentSchool of Pharmacy and Pharmaceutical Science
    Address9500 Gilman Drive #0747
    CA La Jolla 92093
    Phone858-822-3404
    vCardDownload vCard

      Collapse Research 
      Collapse Research Activities and Funding
      Structure, Dynamics and Activation Mechanisms of Chemokine Receptors
      NIH/NIGMS U01GM094612Sep 30, 2010 - Jun 30, 2015
      Role: Principal Investigator
      Novel Druggable Exosites in Protein Kinases
      NIH/NIGMS R01GM074832May 1, 2006 - Apr 30, 2011
      Role: Principal Investigator
      Flexible Macromolecular Docking
      NIH/NIGMS R01GM071872Aug 1, 2004 - May 31, 2018
      Role: Principal Investigator
      THEORETICAL PROTEIN STRUCTURE PREDICTION BY HOMOLGY
      NIH/NIGMS R01GM055418Sep 30, 1997 - Aug 31, 2002
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. 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; 5:e3765. PMID: 28948099.
        View in: PubMed
      2. Lam PC, Abagyan R, Totrov M. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. J Comput Aided Mol Des. 2017 Sep 08. PMID: 28887659.
        View in: PubMed
      3. Shi D, Svetlov D, Abagyan R, Artsimovitch I. Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor. Nucleic Acids Res. 2017 Sep 06; 45(15):8835-8843. PMID: 28605514.
        View in: PubMed
      4. Long T, Rojo-Arreola L, Shi D, El-Sakkary N, Jarnagin K, Rock F, Meewan M, Rascón AA, 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; 11(7):e0005680. PMID: 28704396.
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      5. Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity. 2017 Jun 20; 46(6):1005-1017.e5. PMID: 28636951.
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      6. Sun N, Lu YJ, Chan FY, Du RL, Zheng YY, Zhang K, So LY, Abagyan R, Zhuo C, Leung YC, Wong KY. A Thiazole Orange Derivative Targeting the Bacterial Protein FtsZ Shows Potent Antibacterial Activity. Front Microbiol. 2017; 8:855. PMID: 28553278.
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      7. Subbotina A, Ravna AW, Lysaa RA, Abagyan R, Bugno R, Sager G. Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux. J Pharm Pharmacol. 2017 Jun; 69(6):675-683. PMID: 28211580.
        View in: PubMed
      8. Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satala G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ. From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. J Chem Inf Model. 2017 Feb 27; 57(2):311-321. PMID: 28055203.
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      9. Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 2017 Jan 18; 8:14135. PMID: 28098154.
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      10. Ngo T, Ilatovskiy AV, Stewart AG, Coleman JL, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ. Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2017 Feb; 13(2):235-242. PMID: 27992882.
        View in: PubMed
      11. Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, Handel TM. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature. 2016 12 15; 540(7633):458-461. PMID: 27926736.
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      12. 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. Correction to Environmental Photochemistry of Altrenogest: Photoisomerization to a Bioactive Product with Increased Environmental Persistence via Reversible Photohydration. Environ Sci Technol. 2016 Sep 20; 50(18):10292. PMID: 27604407.
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      13. Liu HC, Goldenberg A, Chen Y, Lun C, Wu W, Bush KT, Balac N, Rodriguez P, Abagyan R, Nigam SK. Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach. J Pharmacol Exp Ther. 2016 Oct; 359(1):215-29. PMID: 27488918.
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      14. Quinti L, Casale M, Moniot S, Pais TF, Van Kanegan MJ, Kaltenbach LS, Pallos J, Lim RG, Naidu SD, Runne H, Meisel L, Rauf NA, Leyfer D, Maxwell MM, Saiah E, Landers JE, Luthi-Carter R, Abagyan R, Dinkova-Kostova AT, Steegborn C, Marsh JL, Lo DC, Thompson LM, Kazantsev AG. SIRT2- and NRF2-Targeting Thiazole-Containing Compound with Therapeutic Activity in Huntington's Disease Models. Cell Chem Biol. 2016 Jul 21; 23(7):849-61. PMID: 27427231.
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      15. 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. Environmental Photochemistry of Altrenogest: Photoisomerization to a Bioactive Product with Increased Environmental Persistence via Reversible Photohydration. Environ Sci Technol. 2016 Jul 19; 50(14):7480-8. PMID: 27356268.
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      16. Pallara C, Rueda M, Abagyan R, Fernández-Recio J. Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters. J Chem Theory Comput. 2016 Jul 12; 12(7):3236-49. PMID: 27294484.
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      17. Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A. Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor. Cell Res. 2016 May; 26(5):574-92. PMID: 27002221; PMCID: PMC4856764 [Available on 05/01/17].
      18. Ngo T, Kufareva I, Coleman JLj, Graham RM, Abagyan R, Smith NJ. Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol. 2016 Oct; 173(20):2934-51. PMID: 26837045.
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      19. Parsonage D, Sheng F, Hirata K, Debnath A, McKerrow JH, Reed SL, Abagyan R, Poole LB, Podust LM. 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. PMID: 26876147; PMCID: PMC5003402 [Available on 05/01/17].
      20. Bennett BC, Purdy MD, Baker KA, Acharya C, McIntire WE, Stevens RC, Zhang Q, Harris AL, Abagyan R, Yeager M. An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels. Nat Commun. 2016 Jan 12; 7:8770. PMID: 26753910; PMCID: PMC4730032.
      21. Dong M, Lam PC, Orry A, Sexton PM, Christopoulos A, Abagyan R, Miller LJ. 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. PMID: 26740626; PMCID: PMC4777851 [Available on 03/04/17].
      22. Desai AJ, Lam PC, Orry A, Abagyan R, Christopoulos A, Sexton PM, Miller LJ. 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. PMID: 26654202; PMCID: PMC4790425.
      23. Ali TB, Schleret TR, Reilly BM, Chen WY, Abagyan R. Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada. PLoS One. 2015; 10(12):e0144337. PMID: 26642212; PMCID: PMC4671709.
      24. Geidl S, Bouchal T, Racek T, Svobodová Vareková R, Hejret V, Krenek A, Abagyan R, Koca J. High-quality and universal empirical atomic charges for chemoinformatics applications. J Cheminform. 2015; 7:59. PMID: 26633997; PMCID: PMC4667495.
      25. Lenoir M, Kufareva I, Abagyan R, Overduin M. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. Membranes (Basel). 2015 Oct 23; 5(4):646-63. PMID: 26512702; PMCID: PMC4704004.
      26. Wu W, Bush KT, Liu HC, Zhu C, Abagyan R, Nigam SK. Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors. Drug Metab Dispos. 2015 Dec; 43(12):1855-63. PMID: 26358290; PMCID: PMC4658493 [Available on 12/01/16].
      27. Skowronska-Krawczyk D, Zhao L, Zhu J, Weinreb RN, Cao G, Luo J, Flagg K, Patel S, Wen C, Krupa M, Luo H, Ouyang H, Lin D, Wang W, Li G, Xu Y, Li O, Chung C, Yeh E, Jafari M, Ai M, Zhong Z, Shi W, Zheng L, Krawczyk M, Chen D, Shi C, Zin C, Zhu J, Mellon PL, Gao W, Abagyan R, Zhang L, Sun X, Zhong S, Zhuo Y, Rosenfeld MG, Liu Y, Zhang K. P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Mol Cell. 2015 Sep 17; 59(6):931-40. PMID: 26365380; PMCID: PMC4648709.
      28. 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. Corrigendum: Lanosterol reverses protein aggregation in cataracts. Nature. 2015 Oct 22; 526(7574):595. PMID: 26308894.
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      29. Zhao L, Chen XJ, Zhu J, Xi YB, Yang X, Hu LD, Ouyang H, Patel SH, Jin X, Lin D, Wu F, Flagg K, Cai H, Li G, Cao G, Lin Y, Chen D, Wen C, Chung C, Wang Y, Qiu A, Yeh E, Wang W, Hu X, Grob S, Abagyan R, Su Z, Tjondro HC, Zhao XJ, Luo H, Hou R, Jefferson J, Perry P, Gao W, Kozak I, Granet D, Li Y, Sun X, Wang J, Zhang L, Liu Y, Yan YB, Zhang K. Lanosterol reverses protein aggregation in cataracts. Nature. 2015 Jul 30; 523(7562):607-11. PMID: 26200341.
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      30. Geidl S, Svobodová Vareková R, Bendová V, Petrusek L, Ionescu CM, Jurka Z, Abagyan R, Koca J. How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? J Chem Inf Model. 2015 Jun 22; 55(6):1088-97. PMID: 26010215.
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      31. Husby J, Bottegoni G, Kufareva I, Abagyan R, Cavalli A. Structure-based predictions of activity cliffs. J Chem Inf Model. 2015 May 26; 55(5):1062-76. PMID: 25918827; PMCID: PMC4553268.
      32. 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. 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. PMID: 25816021.
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      33. Lo IC, Gupta V, Midde KK, Taupin V, Lopez-Sanchez I, Kufareva I, Abagyan R, Randazzo PA, Farquhar MG, Ghosh P. Activation of Gai at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling. Dev Cell. 2015 Apr 20; 33(2):189-203. PMID: 25865347; PMCID: PMC4415880.
      34. Arnautova YA, Abagyan R, Totrov M. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins. J Chem Theory Comput. 2015 May 12; 11(5):2167-2186. PMID: 25999804.
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      35. Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science. 2015 Mar 06; 347(6226):1117-22. PMID: 25612609; PMCID: PMC4362693.
      36. Mayevu NM, Choe H, Abagyan R, Seong JY, Millar RP, Katz AA, Flanagan CA. Histidine(7.36(305)) in the conserved peptide receptor activation domain of the gonadotropin releasing hormone receptor couples peptide binding and receptor activation. Mol Cell Endocrinol. 2015 Feb 15; 402:95-106. PMID: 25583361.
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      37. Kufareva I, Handel TM, Abagyan R. Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol. 2015; 1335:295-311. PMID: 26260608; PMCID: PMC4551442.
      38. Giacoppo JO, C C França T, Kuca K, da Cunha EF, Abagyan R, Mancini DT, Ramalho TC. Molecular modeling and in vitro reactivation study between the oxime BI-6 and acetylcholinesterase inhibited by different nerve agents. J Biomol Struct Dyn. 2015 Sep; 33(9):2048-58. PMID: 25407587.
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      39. Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM. Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):E5363-72. PMID: 25468967; PMCID: PMC4273337.
      40. Dong M, Vattelana AM, Lam PC, Orry AJ, Abagyan R, Christopoulos A, Sexton PM, Haines DR, Miller LJ. Development of a highly selective allosteric antagonist radioligand for the type 1 cholecystokinin receptor and elucidation of its molecular basis of binding. Mol Pharmacol. 2015 Jan; 87(1):130-40. PMID: 25319540; PMCID: PMC4279081.
      41. Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M. Discovery of novel membrane binding structures and functions. Biochem Cell Biol. 2014 Dec; 92(6):555-63. PMID: 25394204; PMCID: PMC4267288.
      42. Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P. Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Mol Biol Cell. 2014 Nov 05; 25(22):3654-71. PMID: 25187647; PMCID: PMC4230624.
      43. Wang Y, Chan FY, Sun N, Lui HK, So PK, Yan SC, Chan KF, Chiou J, Chen S, Abagyan R, Leung YC, Wong KY. Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors. Chem Biol Drug Des. 2014 Dec; 84(6):685-96. PMID: 24890564.
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      44. Shmelkov E, Grigoryan A, Krachmarov C, Abagyan R, Cardozo T. 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. PMID: 25051095; PMCID: PMC4151074.
      45. Kufareva I, Katritch V, Stevens RC, Abagyan R. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. 2014 Aug 05; 22(8):1120-1139. PMID: 25066135; PMCID: PMC4126895.
      46. McRobb FM, Kufareva I, Abagyan R. In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor a. Toxicol Sci. 2014 Sep; 141(1):188-97. PMID: 24928891; PMCID: PMC4271121.
      47. 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. Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity. PLoS One. 2014; 9(5):e97514. PMID: 24824618; PMCID: PMC4019636.
      48. Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ. Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model. 2014 Mar 24; 54(3):933-43. PMID: 24521202; PMCID: PMC3982395.
      49. 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. A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 2014; 9(1):e81454. PMID: 24489642; PMCID: PMC3904831.
      50. McRobb FM, Sahagún V, Kufareva I, Abagyan R. In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol. 2014; 48(3):1964-72. PMID: 24392850; PMCID: PMC3951377.
      51. Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R. PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):717-23. PMID: 24406170; PMCID: PMC3975830.
      52. Matos KS, da Cunha EF, Abagyan R, Ramalho TC. Computational evidence for the reactivation process of human acetylcholinesterase inhibited by carbamates. Comb Chem High Throughput Screen. 2014; 17(6):554-64. PMID: 24344993.
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      53. Chen YC, Totrov M, Abagyan R. Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. Future Med Chem. 2014; 6(16):1741-55. PMID: 25407367; PMCID: PMC4285145.
      54. Rueda M, Orozco M, Totrov M, Abagyan R. BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC Struct Biol. 2013 Dec 13; 13:32. PMID: 24330655; PMCID: PMC3924234.
      55. Kennedy DP, McRobb FM, Leonhardt SA, Purdy M, Figler H, Marshall MA, Chordia M, Figler R, Linden J, Abagyan R, Yeager M. The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers. Mol Pharmacol. 2014 Feb; 85(2):301-9. PMID: 24217444; PMCID: PMC3913357.
      56. Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW. Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor Biol Med Model. 2013 Sep 14; 10:56. PMID: 24034446; PMCID: PMC3848485.
      57. Lane JR, Chubukov P, Liu W, Canals M, Cherezov V, Abagyan R, Stevens RC, Katritch V. Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol. 2013 Dec; 84(6):794-807. PMID: 24021214; PMCID: PMC3834142.
      58. 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. 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. PMID: 23848971.
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      59. Ilatovskiy AV, Abagyan R, Kufareva I. Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. Int J Quantum Chem. 2013 Jun 15; 113(12):1669-1675. PMID: 25414519.
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      60. Harikumar KG, Cawston EE, Lam PC, Patil A, Orry A, Henke BR, Abagyan R, Christopoulos A, Sexton PM, Miller LJ. Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. J Biol Chem. 2013 Jul 19; 288(29):21082-95. PMID: 23754289; PMCID: PMC3774375.
      61. 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. PMID: 23664863; PMCID: PMC4129370.
      62. 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. Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors. Chem Biol Drug Des. 2013 Jun; 81(6):695-706. PMID: 23574807; PMCID: PMC3665732.
      63. Vareková RS, Geidl S, Ionescu CM, Skrehota O, Bouchal T, Sehnal D, Abagyan R, Koca J. Predicting p Ka values from EEM atomic charges. J Cheminform. 2013 Apr 10; 5(1):18. PMID: 23574978; PMCID: PMC3663834.
      64. 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. PMID: 23437089; PMCID: PMC3577790.
      65. 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. PMID: 23625495; PMCID: PMC4091634.
      66. 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. Designing Endocrine Disruption Out of the Next Generation of Chemicals. Green Chem. 2013 Jan; 15(1):181-198. PMID: 25110461.
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      67. 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 01; 12(1):25-34. PMID: 23237917; PMCID: PMC3723354.
      68. 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. PMID: 23092247; PMCID: PMC4074518.
      69. 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. PMID: 22954387; PMCID: PMC3474531.
      70. 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. PMID: 22947092; PMCID: PMC3478405.
      71. 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. PMID: 22964305; PMCID: PMC3509059.
      72. 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-a. Angew Chem Int Ed Engl. 2012 Sep 03; 51(36):9010-4. PMID: 22807261.
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      73. 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. PMID: 22569591; PMCID: PMC3398187.
      74. Chan FY, Neves MA, Sun N, Tsang MW, Leung YC, Chan TH, Abagyan R, Wong KY. Validation of the AmpC ß-lactamase binding site and identification of inhibitors with novel scaffolds. J Chem Inf Model. 2012 May 25; 52(5):1367-75. PMID: 22559726.
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      75. 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. PMID: 22486652; PMCID: PMC3479662.
      76. 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. PMID: 22497303; PMCID: PMC3613333.
      77. 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. PMID: 22467877; PMCID: PMC3365725.
      78. 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. PMID: 22380603; PMCID: PMC4181661.
      79. Jaronczyk M, Wolosewicz 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. PMID: 22309909; PMCID: PMC3365592.
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      83. 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. PMID: 23116466; PMCID: PMC4085113.
      84. Abagyan R. Computational chemistry in 25 years. J Comput Aided Mol Des. 2012 Jan; 26(1):9-10. PMID: 22160588.
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      85. 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. PMID: 22080553; PMCID: PMC3245087.
      86. 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. PMID: 22071255; PMCID: PMC3357065.
      87. Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P. Tyrosine phosphorylation of the Ga-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal. 2011 Sep 27; 4(192):ra64. PMID: 21954290; PMCID: PMC4226136.
      88. 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. PMID: 21904908; PMCID: PMC4175375.
      89. Katritch V, Abagyan R. GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci. 2011 Nov; 32(11):637-43. PMID: 21903279; PMCID: PMC3200445.
      90. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. 2011 Aug 10; 19(8):1108-26. PMID: 21827947; PMCID: PMC3154726.
      91. 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. PMID: 21761919.
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      92. 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. PMID: 21742260; PMCID: PMC3134789.
      93. 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. PMID: 21697825; PMCID: PMC3131495.
      94. 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. PMID: 21625529; PMCID: PMC3098722.
      95. 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 08; 286(27):23888-99. PMID: 21566140; PMCID: PMC3129170.
      96. 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. PMID: 21509537.
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      97. 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 06; 286(18):15895-907. PMID: 21454562; PMCID: PMC3091199.
      98. Arnautova YA, Abagyan R, 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. PMID: 21069716; PMCID: PMC3057902.
      99. 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 07; 47(9):2511-3. PMID: 21240405.
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      100. 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. PMID: 20929726; PMCID: PMC3074590.
      101. 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 01; 26(21):2784-5. PMID: 20871105; PMCID: PMC2981495.
      102. 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. PMID: 20669948; PMCID: PMC2923663.
      103. 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. PMID: 20575553.
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      104. 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. PMID: 20663531; PMCID: PMC2942080.
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      106. 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. PMID: 20534345; PMCID: PMC2884008.
      107. 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. PMID: 20441222; PMCID: PMC2874095.
      108. 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. PMID: 20455005; PMCID: PMC2881208.
      109. Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL. Structure-based discovery of natural-product-like TNF-a inhibitors. Angew Chem Int Ed Engl. 2010 Apr 06; 49(16):2860-4. PMID: 20235259; PMCID: PMC4162403.
      110. Grigoryan AV, Kufareva I, Totrov M, Abagyan R. Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des. 2010 Mar; 24(3):173-82. PMID: 20229197; PMCID: PMC2858276.
      111. 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. PMID: 20095623; PMCID: PMC2826142.
      112. 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):9919-31. PMID: 20100828; PMCID: PMC2843239.
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      115. 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 01; 70(1):329-37. PMID: 19996284.
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      116. 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 07; 15(47):13008-21. PMID: 19876976.
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      118. 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. PMID: 19847312; PMCID: PMC2762615.
      119. 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. PMID: 19719119; PMCID: PMC3289977.
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      121. 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. PMID: 19353579; PMCID: PMC2693451.
      122. 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. PMID: 19441839; PMCID: PMC3443625.
      123. 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. PMID: 19429716; PMCID: PMC2713122.
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      125. 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 08; 284(19):13185-92. PMID: 19240028; PMCID: PMC2676050.
      126. Nicola G, Abagyan R. Structure-based approaches to antibiotic drug discovery. Curr Protoc Microbiol. 2009 Feb; Chapter 17:Unit17.2. PMID: 19235149.
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      131. 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. PMID: 19053777; PMCID: PMC2669721.
      132. 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. PMID: 18260112; PMCID: PMC4162409.
      133. 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. PMID: 18805032.
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      134. Kovacs JA, Yeager M, Abagyan R. Damped-dynamics flexible fitting. Biophys J. 2008 Oct; 95(7):3192-207. PMID: 18586844; PMCID: PMC2547429.
      135. 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. PMID: 18383062.
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      136. 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. PMID: 18467541; PMCID: PMC3879803.
      137. 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. PMID: 18333758; PMCID: PMC2660599.
      138. 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. PMID: 18302357.
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      141. Cavasotto CN, Orry AJ, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O'Neill KA, Hine H, Burton MS, Voigt JH, Abagyan R, Bayne ML, Monsma FJ. 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. PMID: 18198821.
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      142. 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. PMID: 18003900; PMCID: PMC2141826.
      143. 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. PMID: 17960327.
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      144. 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 01; 50(22):5330-8. PMID: 17924613; PMCID: PMC2531295.
      145. 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 01; 50(22):5357-63. PMID: 17918823; PMCID: PMC2631427.
      146. 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. PMID: 17897949; PMCID: PMC4370777.
      147. 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 09; 282(45):32834-43. PMID: 17827151.
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      148. 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. PMID: 17606915; PMCID: PMC1924583.
      149. 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. PMID: 17588900.
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      150. 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. PMID: 17496035; PMCID: PMC1959528.
      151. 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. PMID: 17497806.
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      154. 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 06; 358(3):686-91. PMID: 17509532; PMCID: PMC1987361.
      155. 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. PMID: 17381074; PMCID: PMC2580722.
      156. 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. PMID: 17524457; PMCID: PMC2819402.
      157. Garzón JI, Kovacs J, Abagyan R, Chacón P. DFprot: a webtool for predicting local chain deformability. Bioinformatics. 2007 Apr 01; 23(7):901-2. PMID: 17277334.
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      158. 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. PMID: 17165815; PMCID: PMC3435108.
      159. 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. PMID: 17150992.
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      160. 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. PMID: 17105344; PMCID: PMC1618416.
      161. Budagyan L, Abagyan R. Weighted quality estimates in machine learning. Bioinformatics. 2006 Nov 01; 22(21):2597-603. PMID: 16935929.
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      162. 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. PMID: 16844690.
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      163. 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. PMID: 16873024.
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      164. 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. PMID: 16470819.
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      165. Orry AJ, Abagyan R, Cavasotto CN. Structure-based development of target-specific compound libraries. Drug Discov Today. 2006 Mar; 11(5-6):261-6. PMID: 16580603.
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      166. 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 01; 78(3):779-87. PMID: 16448051.
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      167. Cavasotto CN, Ortiz MA, Abagyan R, Piedrafita FJ. In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. Bioorg Med Chem Lett. 2006 Apr 01; 16(7):1969-74. PMID: 16413185.
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      168. 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. PMID: 16406633.
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      169. 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 01; 48(24):7781-8. PMID: 16302817.
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      170. 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. PMID: 16404815.
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      171. 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. PMID: 16267691.
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      172. Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins. 2005 Aug 15; 60(3):353-66. PMID: 15906321.
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      173. 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 07; 280(40):34073-9. PMID: 16079145.
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      174. Fernández-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins. 2005 Aug 01; 60(2):308-13. PMID: 15981266.
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      175. Cavasotto CN, Kovacs JA, Abagyan R. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc. 2005 Jul 06; 127(26):9632-40. PMID: 15984891.
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      176. Forino M, Johnson S, Wong TY, Rozanov DV, Savinov AY, Li W, Fattorusso R, Becattini B, Orry AJ, Jung D, Abagyan R, 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 05; 102(27):9499-504. PMID: 15983377; PMCID: PMC1160517.
      177. 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. PMID: 15757999.
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      178. Bordner AJ, Abagyan R. REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics. 2005 May 15; 21(10):2315-21. PMID: 15749694.
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      179. Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 2005 Jan 01; 58(1):134-43. PMID: 15495260.
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      180. Cardozo T, Abagyan R. Druggability of SCF ubiquitin ligase-protein interfaces. Methods Enzymol. 2005; 399:634-53. PMID: 16338386.
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      181. Bordner AJ, Abagyan R. Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins. 2004 Nov 01; 57(2):400-13. PMID: 15340927.
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      182. Kovacs JA, Chacón P, Abagyan R. Predictions of protein flexibility: first-order measures. Proteins. 2004 Sep 01; 56(4):661-8. PMID: 15281119.
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      183. 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. PMID: 15317450.
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      184. 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. PMID: 15149689.
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      185. Marsden B, Abagyan R. SAD--a normalized structural alignment database: improving sequence-structure alignments. Bioinformatics. 2004 Oct 12; 20(15):2333-44. PMID: 15087320.
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      186. Cavasotto CN, Abagyan R. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol. 2004 Mar 12; 337(1):209-25. PMID: 15001363.
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      187. 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. PMID: 14687579.
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      188. An J, Totrov M, Abagyan R. Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform. 2004; 15(2):31-41. PMID: 15706489.
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      189. Bursulaya BD, Totrov M, Abagyan R, Brooks CL. Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des. 2003 Nov; 17(11):755-63. PMID: 15072435.
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      190. Schapira M, Abagyan R, Totrov M. Nuclear hormone receptor targeted virtual screening. J Med Chem. 2003 Jul 03; 46(14):3045-59. PMID: 12825943.
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      191. Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins. 2003 Jul 01; 52(1):113-7. PMID: 12784376.
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      192. 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. PMID: 12777627; PMCID: PMC165879.
      193. Cavasotto CN, Orry AJ, Abagyan R. Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins. 2003 May 15; 51(3):423-33. PMID: 12696053.
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      194. Zhou Y, Abagyan R. Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel. 2003 May; 6(3):339-45. PMID: 12833666.
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      195. 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. PMID: 12542701.
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      196. 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. PMID: 12497604.
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      197. 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 04; 298(5591):216-8. PMID: 12364807.
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      198. Fernández-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci. 2002 Feb; 11(2):280-91. PMID: 11790838; PMCID: PMC2373434.
      199. Zhou Y, Abagyan R. Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics. 2002; 3:3. PMID: 11835687; PMCID: PMC65509.
      200. Schapira M, Abagyan R, Totrov M. Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol. 2002; 2:1. PMID: 11860617; PMCID: PMC65631.
      201. Brive L, Abagyan R. Computational structural proteomics. Ernst Schering Res Found Workshop. 2002; (38):149-66. PMID: 12061000.
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      202. Fernandez-Recio J, Totrov M, Abagyan R. Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput. 2002; 552-63. PMID: 11928507.
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      203. Abagyan R, Totrov M. High-throughput docking for lead generation. Curr Opin Chem Biol. 2001 Aug; 5(4):375-82. PMID: 11470599.
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      204. Schapira M, Raaka BM, Samuels HH, Abagyan R. In silico discovery of novel retinoic acid receptor agonist structures. BMC Struct Biol. 2001; 1:1. PMID: 11405897; PMCID: PMC32304.
      205. Norledge BV, Lambeir AM, Abagyan R, 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. PMID: 11151009.
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      206. 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. PMID: 11455546.
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      207. Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan R, 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. PMID: 10921774.
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      208. 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. PMID: 10816526; PMCID: PMC97657.
      209. 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. PMID: 10756107.
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      210. 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. PMID: 10779498; PMCID: PMC310859.
      211. 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. PMID: 10666333.
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      212. 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 01; 97(3):1008-13. PMID: 10655475; PMCID: PMC15503.
      213. Cardozo T, Batalov S, Abagyan R. Estimating local backbone structural deviation in homology models. Comput Chem. 2000 Jan; 24(1):13-31. PMID: 10642877.
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      214. 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. PMID: 10490654; PMCID: PMC84712.
      215. 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. PMID: 10404595.
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      216. 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. PMID: 10398408.
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      217. 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. PMID: 10196177.
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      218. 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.
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      219. 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. PMID: 9736615; PMCID: PMC1170863.
      220. 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. PMID: 9768844.
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      221. Patel IR, Attur MG, Patel RN, Stuchin SA, Abagyan R, 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 01; 160(9):4570-9. PMID: 9574564.
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      222. Zhou Y, Abagyan R. How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold Des. 1998; 3(6):513-22. PMID: 9889165.
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      223. Maiorov V, Abagyan R. Energy strain in three-dimensional protein structures. Fold Des. 1998; 3(4):259-69. PMID: 9710569.
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      224. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan R, 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. PMID: 9402066.
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      225. Abagyan R, Batalov S. Do aligned sequences share the same fold? J Mol Biol. 1997 Oct 17; 273(1):355-68. PMID: 9367768.
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      226. 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. PMID: 9336837; PMCID: PMC2143572.
      227. 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 05; 36(31):9423-8. PMID: 9235986.
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      228. Koonin EV, Abagyan R. TSG101 may be the prototype of a class of dominant negative ubiquitin regulators. Nat Genet. 1997 Aug; 16(4):330-1. PMID: 9241264.
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      229. Abagyan R, Totrov MM. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol. 1997 May 09; 268(3):678-85. PMID: 9171291.
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      230. Maiorov V, Abagyan R. A new method for modeling large-scale rearrangements of protein domains. Proteins. 1997 Mar; 27(3):410-24. PMID: 9094743.
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      231. 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. PMID: 9034152; PMCID: PMC2196154.
      232. Thanki N, Zeelen JP, Mathieu M, Jaenicke R, Abagyan R, 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. PMID: 9089815.
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      233. Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins. 1997; Suppl 1:215-20. PMID: 9485515.
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      234. 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. PMID: 9485492.
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      235. 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. PMID: 8899296.
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      236. 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. PMID: 8759322.
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      237. 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. PMID: 8605624.
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      238. Totrov M, Abagyan R. The contour-buildup algorithm to calculate the analytical molecular surface. J Struct Biol. 1996 Jan-Feb; 116(1):138-43. PMID: 8742735.
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      239. Cardozo T, Totrov M, Abagyan R. Homology modeling by the ICM method. Proteins. 1995 Nov; 23(3):403-14. PMID: 8710833.
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      240. Houbrechts A, Moreau B, Abagyan R, Mainfroid V, Préaux G, Lamproye A, Poncin A, Goormaghtigh E, Ruysschaert JM, Martial JA. 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. PMID: 7479687.
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      241. 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. PMID: 7952893.
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      242. Abagyan R, Frishman D, Argos P. Recognition of distantly related proteins through energy calculations. Proteins. 1994 Jun; 19(2):132-40. PMID: 8090707.
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      243. 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. PMID: 7656055.
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      244. 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. PMID: 8108439; PMCID: PMC43190.
      245. 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. PMID: 8289329.
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      246. Kuznetsov DA, Abagyan R. A technique for identifying atoms from a screen image. J Mol Graph. 1993 Dec; 11(4):245-7. PMID: 8136327.
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      247. Abagyan R. Towards protein folding by global energy optimization. FEBS Lett. 1993 Jun 28; 325(1-2):17-22. PMID: 8513887.
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      248. 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 05; 231(3):849-60. PMID: 8515455.
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      249. Gibson TJ, Thompson JD, Abagyan R. 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. PMID: 8433970.
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      250. 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. PMID: 1593634.
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      251. Abagyan R, 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. PMID: 2315048; PMCID: PMC330354.
      252. Gromova II, Buchman VL, Abagyan R, 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. PMID: 2155407; PMCID: PMC333473.
      253. Eisenhaber F, Tumanyan VG, Abagyan R. 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. PMID: 2265229.
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      254. Abagyan R, 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. PMID: 2818856.
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      255. Mazur AK, Abagyan R. 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. PMID: 2619942.
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      256. Abagyan R, 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. PMID: 2619943.
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      257. Chuprina VP, Abagyan R. Structural basis of stable bending in DNA containing An tracts. Different types of bending. J Biomol Struct Dyn. 1988 Aug; 6(1):121-38. PMID: 3271514.
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      258. Abagyan R, 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. PMID: 3271511.
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      259. Chuprina VP, Abagyan R. Anomalous properties of adenine.thymine tracts. Nature. 1988 Mar 10; 332(6160):117. PMID: 3347251.
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      260. Ivanitskii GR, Esipova NG, Abagyan R, Shnol' SE. [Block improvement of the genetic text as a factor of acceleration of biological evolution]. Biofizika. 1985 May-Jun; 30(3):418-21. PMID: 4027270.
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      261. Abagyan R, Tumanian VG, Esipova NG. [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. PMID: 6548632.
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      262. Abagyan R. [Diffraction from the alternating helix]. Biofizika. 1983 May-Jun; 28(3):388-92. PMID: 6871260.
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      263. Abagyan R. [Arrangement of molecular packing of collagen in fibrils]. Biofizika. 1983 May-Jun; 28(3):498-500. PMID: 6871272.
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      264. Rogulenkova VN, Abagyan R, Tumanian VG, Esipova NG. [Diffraction effects on x-rays of the oligotripeptide (Gly-Pro-Pro)10, isomorphic to collagen]. Biofizika. 1981 Jul-Aug; 26(4):734-6. PMID: 7284464.
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