RubenAbagyan 185x245Professor, UCSD

Skaggs School of Pharmacy and Pharmaceutical Sciences

Computational Drug Discovery Core Director, CDIPD

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The Abagyan research laboratory develops and applies methods for molecular modeling, structure based discovery and optimization of drug candidates, target identification, large scale bio- and chemo-informatics. We have introduced and developed the structural Pocketomes for different organisms and used it for repurposing of drugs for different pathogens and indications. We are collaborating with the CDIPD Core Faculties, Drs. McKerrow, Podust, Caffrey, Siqueira-Net and Debnath, on various projects related to the CDIPD mission.

Dr. Abagyan got his PhD in biophysics from the Moscow State University and his tenure in biochemistry and mathematics from New York University and the Courant Institute of Mathematics. He was a Director of Computational Sciences at the Novartis Institute for Functional Genomics, and a Professor at the Scripps Research Institute in La Jolla before joining the Skaggs School of Pharmacy and Pharmaceutical Sciences at UCSD.


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 Oct 17. doi: 10.1021/acsinfecdis.9b00227. [Epub ahead of print] Shi D, Chahal KK, Oto P, Nothias LF, Debnath A, McKerrow JH, Podust LM, Abagyan R.

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. eCollection 2017 Dec. Debnath A, Calvet CM, Jennings G, Zhou W, Aksenov A, Luth MR, Abagyan R, Nes WD, McKerrow JH, Podust LM.

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. eCollection 2017 Jul. 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.

Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux. J Pharm Pharmacol. 2017 Feb 17. doi: 10.1111/jphp.12693. [Epub ahead of print] Subbotina A, Ravna AW, Lysaa RA, Abagyan R, Bugno R, Sager G.

Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 2017 Jan 18;8:14135. doi: 10.1038/ncomms14135. Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM.

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT(1A) Receptor Case Study. J Chem Inf Model. 2017 Feb 27;57(2):311-321. doi: 10.1021/acs.jcim.6b00263. Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satała G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ.

Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2017 Feb;13(2):235-242. doi: 10.1038/nchembio.2266. Ngo T, Ilatovskiy AV, Stewart AG, Coleman JL, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ.

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature. 2016 Dec 15;540(7633):458-461. doi: 10.1038/nature20605. 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.

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. doi: 10.1021/acs.est.6b04213. No abstract available. 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.

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. doi: 10.1124/jpet.116.232660. Liu HC, Goldenberg A, Chen Y, Lun C, Wu W, Bush KT, Balac N, Rodriguez P, Abagyan R, Nigam SK.

An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network. J Biol Chem. 2016 Sep 9;291(37):19474-86. doi: 10.1074/jbc.M116.745216. Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK.

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. doi: 10.1016/j.chembiol.2016.05.015. 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, et al.

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. doi: 10.1021/acs.est.6b02608. 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.

Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters. J Chem Theory Comput. 2016 Jul 12;12(7):3236-49. doi: 10.1021/acs.jctc.6b00204. Pallara C, Rueda M, Abagyan R, Fernández-Recio J.

Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor. Cell Res. 2016 May;26(5):574-92. doi: 10.1038/cr.2016.36. Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A.

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. doi: 10.1016/j.jsb.2016.02.015. Epub 2016 Feb 12. Parsonage D, Sheng F, Hirata K, Debnath A, McKerrow JH, Reed SL, Abagyan R, Poole LB, Podust LM.

Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol. 2016 Oct;173(20):2934-51. doi: 10.1111/bph.13452. Review. Ngo T, Kufareva I, Coleman JLj, Graham RM, Abagyan R, Smith NJ.

An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels. Nat Commun. 2016 Jan 12;7:8770. doi: 10.1038/ncomms9770. Bennett BC, Purdy MD, Baker KA, Acharya C, McIntire WE, Stevens RC, Zhang Q, Harris AL, Abagyan R, Yeager M.

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 4;291(10):5172-84. doi: 10.1074/jbc.M115.706010. Dong M, Lam PC, Orry A, Sexton PM, Christopoulos A, Abagyan R, 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. doi: 10.1021/acs.jmedchem.5b01110. Desai AJ, Lam PC, Orry A, Abagyan R, Christopoulos A, Sexton PM, Miller LJ.

Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada. PLoS One. 2015 Dec 7;10(12):e0144337. doi: 10.1371/journal.pone.0144337. Ali TB, Schleret TR, Reilly BM, Chen WY, Abagyan R.

High-quality and universal empirical atomic charges for chemoinformatics applications. J Cheminform. 2015 Dec 2;7:59. doi: 10.1186/s13321-015-0107-1. Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J.

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. Membranes (Basel). 2015 Oct 23;5(4):646-63. doi: 10.3390/membranes5040646. Lenoir M, Kufareva I, Abagyan R, Overduin M.

Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors. Drug Metab Dispos. 2015 Dec;43(12):1855-63. doi: 10.1124/dmd.115.065250. Wu W, Bush KT, Liu HC, Zhu C, Abagyan R, Nigam SK.

Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol. 2015;1335:295-311. doi: 10.1007/978-1-4939-2914-6_19. Kufareva I, Handel TM, Abagyan R.

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. doi: 10.1021/ci500758w. Geidl S, Svobodová Vařeková R, Bendová V, Petrusek L, Ionescu CM, Jurka Z, Abagyan R, Koča J.

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins. J Chem Theory Comput. 2015 May 12;11(5):2167-2186. Arnautova YA, Abagyan R, Totrov M.

Structure-based predictions of activity cliffs. J Chem Inf Model. 2015 May 26;55(5):1062-76. doi: 10.1021/ci500742b. Husby J, Bottegoni G, Kufareva I, Abagyan R, Cavalli A.

Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling. Dev Cell. 2015 Apr 20;33(2):189-203. doi: 10.1016/j.devcel.2015.02.009. Lo IC, Gupta V, Midde KK, Taupin V, Lopez-Sanchez I, Kufareva I, Abagyan R, Randazzo PA, Farquhar MG, Ghosh P.

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. doi: 10.1021/ci500598e. 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.

Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science. 2015 Mar 6;347(6226):1117-22. doi: 10.1126/science.1261064. 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.

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. doi: 10.1016/j.mce.2015.01.008. Mayevu NM, Choe H, Abagyan R, Seong JY, Millar RP, Katz AA, Flanagan CA.

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. doi: 10.1073/pnas.1417037111. Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM.

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. doi: 10.1080/07391102.2014.989408. Giacoppo JO, C C França T, Kuča K, da Cunha EF, Abagyan R, Mancini DT, Ramalho TC.

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. Future Med Chem. 2014;6(16):1741-55. doi: 10.4155/fmc.14.113. Chen YC, Totrov M, Abagyan R.

Discovery of novel membrane binding structures and functions. Biochem Cell Biol. 2014 Dec;92(6):555-63. doi: 10.1139/bcb-2014-0074. Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M.

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. doi: 10.1124/mol.114.095430. Dong M, Vattelana AM, Lam PC, Orry AJ, Abagyan R, Christopoulos A, Sexton PM, Haines DR, Miller LJ.

Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Mol Biol Cell. 2014 Nov 5;25(22):3654-71. doi: 10.1091/mbc.E14-05-0978. Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P.

Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. 2014 Aug 5;22(8):1120-39. doi: 10.1016/j.str.2014.06.012. Kufareva I, Katritch V; Participants of GPCR Dock 2013., Stevens RC, Abagyan R.

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. doi: 10.1089/AID.2014.0034. Shmelkov E, Grigoryan A, Krachmarov C, Abagyan R, Cardozo T.

In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. Toxicol Sci. 2014 Sep;141(1):188-97. doi: 10.1093/toxsci/kfu114. McRobb FM, Kufareva I, Abagyan R.

Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors. Chem Biol Drug Des. 2014 Dec;84(6):685-96. doi: 10.1111/cbdd.12361. Wang Y, Chan FY, Sun N, Lui HK, So PK, Yan SC, Chan KF, Chiou J, Chen S, Abagyan R, Leung YC, Wong KY.

Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity. PLoS One. 2014 May 13;9(5):e97514. doi: 10.1371/journal.pone.0097514. 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.

Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model. 2014 Mar 24;54(3):933-43. doi: 10.1021/ci400742s. Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ.

A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 2014 Jan 28;9(1):e81454. doi: 10.1371/journal.pone.0081454. 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.

PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun. 2014 Mar 21;445(4):717-23. doi: 10.1016/j.bbrc.2013.12.132. Acharya C, Kufareva I, Ilatovskiy AV, 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. doi: 10.1021/es404568a. McRobb FM, Sahagún V, Kufareva I, Abagyan R.

Computational evidence for the reactivation process of human acetylcholinesterase inhibited by carbamates. Comb Chem High Throughput Screen. 2014;17(6):554-64. Matos KS, da Cunha EF, Abagyan R, Ramalho TC.

BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC Struct Biol. 2013 Dec 13;13:32. doi: 10.1186/1472-6807-13-32. Rueda M, Orozco M, Totrov M, Abagyan R.

The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers. Mol Pharmacol. 2014 Feb;85(2):301-9. doi: 10.1124/mol.113.088682. Kennedy DP, McRobb FM, Leonhardt SA, Purdy M, Figler H, Marshall MA, Chordia M, Figler R, Linden J, Abagyan R, Yeager M.

Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor Biol Med Model. 2013 Sep 14;10:56. doi: 10.1186/1742-4682-10-56. Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW.

Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol. 2013 Dec;84(6):794-807. doi: 10.1124/mol.113.088054. Lane JR, Chubukov P, Liu W, Canals M, Cherezov V, Abagyan R, Stevens RC, Katritch V.

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. doi: 10.1021/ci400203f. 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.

Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. Int J Quantum Chem. 2013 Jun 15;113(12):1669-1675. Ilatovskiy AV, Abagyan R, Kufareva I.

Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. J Biol Chem. 2013 Jul 19;288(29):21082-95. doi: 10.1074/jbc.M113.480715. Harikumar KG, Cawston EE, Lam PC, Patil A, Orry A, Henke BR, Abagyan R, Christopoulos A, Sexton PM, Miller LJ.

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. Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg J.

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. Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM.

Predicting p Ka values from EEM atomic charges. J Cheminform. 2013 Apr 10;5(1):18. doi: 10.1186/1758-2946-5-18. Vařeková RS, Geidl S, Ionescu CM, Skřehota O, Bouchal T, Sehnal D, Abagyan R, Koča J.

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. 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.

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. Erratum in: PLoS One. 2014;9(3):e92488. Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan R, Mensa-Wilmot K.

Designing Endocrine Disruption Out of the Next Generation of Chemicals. Green Chem. 2013 Jan;15(1):181-198. Schug TT, Abagyan R, Blumberg B, Collins TJ, Crews D, DeFur PL, Dickerson SM, Edwards TM, Gore AC, Guillette LJ, Hayes T, Heindel JJ, Moores A, Patisaul HB, Tal TL, Thayer KA, Vandenberg LN, Warner J, Watson CS, Saal FS, Zoeller RT, O'Brien KP, et al.

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. Review. Stevens RC, Cherezov V, Katritch V, Abagyan R, Kuhn P, Rosen H, Wüthrich K.

Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem. 2012;12(17):1869-82. Review. Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R.

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. Review. Montaner S, Kufareva I, Abagyan R, Gutkind JS.

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. Dong M, Xu X, Ball AM, Makhoul JA, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ.

Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization. J Med Chem. 2012 Sep 27;55(18):7998-8006. Wein AN, Williams BN, Liu S, Ermolinsky B, Provenzano D, Abagyan R, Orry A, Leppla SH, Peredelchuk M.

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. Rueda M, Totrov M, Abagyan R.

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. Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DS, Ma VP, Abagyan R, Wong CY, Ma DL.

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. Neves MA, Totrov M, Abagyan R.

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: 10.1021/ci300068m. Chan FY, Neves MA, Sun N, Tsang MW, Leung YC, Chan TH, Abagyan R, Wong KY.

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. Neves MA, Yeager M, Abagyan R.

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. Tosh DK, Phan K, Gao ZG, Gakh AA, Xu F, Deflorian F, Abagyan R, Stevens RC, Jacobson KA, Katritch V.

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: 10.1074/jbc.M111.335646. Cawston EE, Lam PC, Harikumar KG, Dong M, Ball AM, Augustine ML, Akgün E, Portoghese PS, Orry A, Abagyan R, Sexton PM, Miller LJ.

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. Sager G, Ørvoll EØ, Lysaa RA, Kufareva I, Abagyan R, Ravna AW.

Preparation and refinement of model protein-ligand complexes. Methods Mol Biol. 2012;857:351-73. doi: 10.1007/978-1-61779-588-6_16. Orry AJ, Abagyan R.

Methods of protein structure comparison. Methods Mol Biol. 2012;857:231-57. doi: 10.1007/978-1-61779-588-6_10. Kufareva I, Abagyan R.

Ligand-guided receptor optimization. Methods Mol Biol. 2012;857:189-205. doi: 10.1007/978-1-61779-588-6_8. Katritch V, Rueda M, Abagyan R.

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. Jarończyk M, Wołosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z.

Computational chemistry in 25 years. J Comput Aided Mol Des. 2012 Jan;26(1):9-10. doi: 10.1007/s10822-011-9516-z. 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. Kufareva I, Ilatovskiy AV, Abagyan R.

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. Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z, Bojarski AJ, Sylte I.

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. Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P.

GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci. 2011 Nov;32(11):637-43. doi: 10.1016/ Katritch V, 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. Bordner AJ, Zorman B, Abagyan R.

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. Svobodová Vareková R, Geidl S, Ionescu CM, Skrehota O, Kudera M, Sehnal D, Bouchal T, Abagyan R, Huber HJ, Koca J.

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. Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley SK, Darnell RB, Patel DJ.

Structure of the human histamine H1 receptor complex with doxepin. Nature. 2011 Jun 22;475(7354):65-70. doi: 10.1038/nature10236. 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.

Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One. 2011;6(5):e18845. doi: 10.1371/journal.pone.0018845. Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A.

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. Dong M, Lam PC, Pinon DI, Hosohata K, Orry A, Sexton PM, Abagyan R, Miller LJ.

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: 10.1007/s10545-011-9334-4. No abstract available. Lee WH, Yue WW, Raush E, Totrov M, Abagyan R, Oppermann U, Marsden BD.

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. Miller LJ, Chen Q, Lam PC, Pinon DI, Sexton PM, Abagyan R, Dong M.

A natural product-like inhibitor of NEDD8-activating enzyme. Chem Commun (Camb). 2011 Mar 7;47(9):2511-3. doi: 10.1039/c0cc04927a. Leung CH, Chan DS, Yang H, Abagyan R, Lee SM, Zhu GY, Fong WF, Ma DL.

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. 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.

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. Rueda M, Katritch V, Raush E, Abagyan R.

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. Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, Stevens RC.

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. Erratum in: Virology. 2011 Jan 20;409(2):360. Abagyan, Ruben [added]. 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 based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology. 2011 Jan;60(1):108-15. doi: 10.1016/j.neuropharm.2010.07.009. Katritch V, Kufareva I, Abagyan R.

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. Odell LR, Howan D, Gordon CP, Robertson MJ, Chau N, Mariana A, Whiting AE, Abagyan R, Daniel JA, Gorgani NN, Robinson PJ, McCluskey A.

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. 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.

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: 10.1007/s10822-010-9362-4. Park SJ, Kufareva I, 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. Cheltsov AV, Aoyagi M, Aleshin A, Yu EC, Gilliland T, Zhai D, Bobkov AA, Reed JC, Liddington RC, Abagyan R.

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. Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL.

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. doi: 10.1074/jbc.M109.089730. Dong M, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ.

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. Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, 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. Katritch V, Rueda M, Lam PC, Yeager M, 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. Rueda M, Bottegoni G, Abagyan R.

A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway. Cancer Res. 2010 Jan 1;70(1):329-37. doi: 10.1158/0008-5472.CAN-09-3324. Chow KH, Sun RW, Lam JB, Li CK, Xu A, Ma DL, Abagyan R, Wang Y, 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. Wu P, Ma DL, Leung CH, Yan SC, Zhu N, Abagyan R, Che CM.

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. No abstract available. Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD.

A new method for publishing three-dimensional content. PLoS One. 2009 Oct 20;4(10):e7394. doi: 10.1371/journal.pone.0007394. No abstract available. Raush E, Totrov M, Marsden BD, Abagyan R.

The flexible pocketome engine for structural chemogenomics. Methods Mol Biol. 2009;575:249-79. doi: 10.1007/978-1-60761-274-2_11. Abagyan R, Kufareva I.

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. Bisson WH, Koch DC, O'Donnell EF, Khalil SM, Kerkvliet NI, Tanguay RL, Abagyan R, Kolluri SK.

FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics. 2009 Oct 1;25(19):2544-51. doi: 10.1093/bioinformatics/btp447. Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P.

Homology modeling of GPCRs. Methods Mol Biol. 2009;552:97-113. doi: 10.1007/978-1-60327-317-6_7. Simms J, Hall NE, Lam PH, Miller LJ, Christopoulos A, Abagyan R, Sexton PM.

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. Dong M, Lam PC, Pinon DI, Abagyan R, Miller LJ.

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. Rueda M, Bottegoni G, Abagyan R.

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. Gao F, Harikumar KG, Dong M, Lam PC, Sexton PM, Christopoulos A, Bordner A, Abagyan R, Miller LJ.

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. Katritch V, Reynolds KA, Cherezov V, Hanson MA, Roth CB, Yeager M, Abagyan R.

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. Wu YW, Goody RS, Abagyan R, Alexandrov K.

Structure-based approaches to antibiotic drug discovery. Curr Protoc Microbiol. 2009 Feb;Chapter 17:Unit17.2. doi: 10.1002/9780471729259.mc1702s12. Nicola G, 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. Reynolds KA, Katritch V, 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. Bottegoni G, Kufareva I, Totrov M, 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. Kufareva I, Abagyan R.

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. Bisson WH, Abagyan R, Cavasotto CN.

Damped-dynamics flexible fitting. Biophys J. 2008 Oct;95(7):3192-207. doi: 10.1529/biophysj.108.132357. Kovacs JA, Yeager M, Abagyan R.

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. Dong M, Lam PC, Pinon DI, Sexton PM, Abagyan R, Miller LJ.

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. No abstract available. Ma DL, Lai TS, Chan FY, Chung WH, Abagyan R, Leung YC, Wong KY.

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. Nicola G, Smith CA, 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/ Review. Totrov M, Abagyan R.

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. Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S.

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. Bottegoni G, Kufareva I, Totrov M, Abagyan R.

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. Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J.

3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18619-24. Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva I, Abagyan R, Broide DH, Lee J, Raz E.

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J Comput Aided Mol Des. 2007 Oct-Nov;21(10-11):549-58. Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan R, Hruby DE.

De novo discovery of serotonin N-acetyltransferase inhibitors. J Med Chem. 2007 Nov 1;50(22):5330-8. Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA.

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. Mallya M, Phillips RL, Saldanha SA, Gooptu B, Brown SC, Termine DJ, Shirvani AM, Wu Y, Sifers RN, Abagyan R, Lomas DA.

Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem. 2007 Dec 14;282(50):36505-13. Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, Pasquale EB, Kuhn P.

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. Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ.

Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11927-32. Bisson WH, Cheltsov AV, Bruey-Sedano N, Lin B, Chen J, Goldberger N, May LT, Christopoulos A, Dalton JT, Sexton PM, Zhang XK, Abagyan R.

Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science. 2007 Jul 27;317(5837):516-9. Outeiro TF, Kontopoulos E, Altmann SM, Kufareva I, Strathearn KE, Amore AM, Volk CB, Maxwell MM, Rochet JC, McLean PJ, Young AB, Abagyan R, Feany MB, Hyman BT, Kazantsev AG.

Molecular modeling and mutagenesis of gap junction channels. Prog Biophys Mol Biol. 2007 May-Jun;94(1-2):15-28. Review. Kovacs JA, Baker KA, Altenberg GA, Abagyan R, Yeager M.

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. Nicola G, Smith CA, Lucumi E, Kuo MR, Karagyozov L, Fidock DA, Sacchettini JC, Abagyan R.

Self-assembling cannabinomimetics: supramolecular structures of N-alkyl amides. J Nat Prod. 2007 Jun;70(6):1010-5. Raduner S, Bisson W, Abagyan R, Altmann KH, Gertsch J.

Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys J. 2007 Sep 15;93(6):1950-9. Kovacs JA, Yeager M, Abagyan R.

Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol. 2007 Aug;72(2):280-90. Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ.

Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction. Biochemistry. 2007 Apr 17;46(15):4522-31. Dong M, Ding XQ, Thomas SE, Gao F, Lam PC, Abagyan R, Miller LJ.

PIER: protein interface recognition for structural proteomics. Proteins. 2007 May 1;67(2):400-17. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R.

DFprot: a webtool for predicting local chain deformability. Bioinformatics. 2007 Apr 1;23(7):901-2. Garzón JI, Kovacs J, Abagyan R, Chacón P.

Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A. Anal Chem. 2006 Dec 15;78(24):8265-72. Saldanha SA, Kaler G, Cottam HB, Abagyan R, Taylor SS.

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics. 2007 Feb 15;23(4):427-33. Garzón JI, Kovacs J, Abagyan R, Chacón P.

The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol. 2006 Nov;4(11):e362. Malinina L, Malakhova ML, Kanack AT, Lu M, Abagyan R, Brown RE, Patel DJ.

Weighted quality estimates in machine learning. Bioinformatics. 2006 Nov 1;22(21):2597-603. Budagyan L, Abagyan R.

Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-deficient cells. Chem Biol. 2006 Jul;13(7):765-70. Altmann SM, Muryshev A, Fossale E, Maxwell MM, Norflus FN, Fox J, Hersch SM, Young AB, MacDonald ME, Abagyan R, Kazantsev AG.

Defining the CD59-C9 binding interaction. J Biol Chem. 2006 Sep 15;281(37):27398-404. Huang Y, Qiao F, Abagyan R, Hazard S, Tomlinson S.

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins. 2006 May 15;63(3):512-26. Bordner AJ, Abagyan R.

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 2006 Feb 1;78(3):779-87. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G.

METLIN: a metabolite mass spectral database. Ther Drug Monit. 2005 Dec;27(6):747-51. Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G.

Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci. 2006 Feb;31(2):76-8. No abstract available. Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, Marsden BD.

Druggability of SCF ubiquitin ligase-protein interfaces. Methods Enzymol. 2005;399:634-53. Cardozo T, Abagyan R.

Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins. J Med Chem. 2005 Dec 1;48(24):7781-8. Hill T, Odell LR, Edwards JK, Graham ME, McGeachie AB, Rusak J, Quan A, Abagyan R, Scott JL, Robinson PJ, McCluskey A.

Surrogate data--a secure way to share corporate data. J Comput Aided Mol Des. 2005 Sep-Oct;19(9-10):749-64. Tetko IV, Abagyan R, Oprea TI.

Insights into the human CD59 complement binding interface toward engineering new therapeutics. J Biol Chem. 2005 Oct 7;280(40):34073-9. Huang Y, Smith CA, Song H, Morgan BP, Abagyan R, Tomlinson S.

Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins. 2005 Aug 1;60(2):308-13. Fernández-Recio J, Abagyan R, Totrov M.

Statistical analysis and prediction of protein-protein interfaces. Proteins. 2005 Aug 15;60(3):353-66. Bordner AJ, Abagyan R.

Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics. 2005 Jun;4(6):752-61. An J, Totrov M, Abagyan R.

REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics. 2005 May 15;21(10):2315-21. Bordner AJ, Abagyan R.

Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform. 2004;15(2):31-41. An J, Totrov M, Abagyan R.

Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 2005 Jan 1;58(1):134-43. Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R.

Determinants of retinoid X receptor transcriptional antagonism. J Med Chem. 2004 Aug 26;47(18):4360-72. Cavasotto CN, Liu G, James SY, Hobbs PD, Peterson VJ, Bhattacharya AA, Kolluri SK, Zhang XK, Leid M, Abagyan R, Liddington RC, Dawson MI.

Predictions of protein flexibility: first-order measures. Proteins. 2004 Sep 1;56(4):661-8. Kovacs JA, Chacón P, Abagyan R.

Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorg Med Chem Lett. 2004 Jun 21;14(12):3275-8. Hill TA, Odell LR, Quan A, Abagyan R, Ferguson G, Robinson PJ, McCluskey A.

SAD--a normalized structural alignment database: improving sequence-structure alignments. Bioinformatics. 2004 Oct 12;20(15):2333-44. Marsden B, Abagyan R.

Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des. 2003 Nov;17(11):755-63. Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd.

Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol. 2004 Jan 16;335(3):843-65. Fernández-Recio J, Totrov M, Abagyan R.

Algorithms for high-density oligonucleotide array. Curr Opin Drug Discov Devel. 2003 May;6(3):339-45. Review. Zhou Y, Abagyan R.

Nuclear hormone receptor targeted virtual screening. J Med Chem. 2003 Jul 3;46(14):3045-59. Schapira M, Abagyan R, Totrov M.

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7354-9. Schapira M, Raaka BM, Das S, Fan L, Totrov M, Zhou Z, Wilson SR, Abagyan R, Samuels HH.

ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins. 2003 Jul 1;52(1):113-7. Fernández-Recio J, Totrov M, Abagyan R.

The transthyretin-related protein family. Eur J Biochem. 2003 Feb;270(3):518-32. Eneqvist T, Lundberg E, Nilsson L, Abagyan R, Sauer-Eriksson AE.

ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. J Comput Chem. 2003 Jan 30;24(2):254-65. Katritch V, Totrov M, Abagyan R.

Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science. 2002 Oct 4;298(5591):216-8. Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, Winzeler EA.

Computational structural proteomics. Ernst Schering Res Found Workshop. 2002;(38):149-66. Review. No abstract available. Brive L, Abagyan R.

Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput. 2002:552-63. Fernandez-Recio J, Totrov M, Abagyan R.

Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol. 2002;2:1. Schapira M, Abagyan R, Totrov M.

Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics. 2002;3:3. Zhou Y, Abagyan R.

Soft protein-protein docking in internal coordinates. Protein Sci. 2002 Feb;11(2):280-91. Fernández-Recio J, Totrov M, Abagyan R.

High-throughput docking for lead generation. Curr Opin Chem Biol. 2001 Aug;5(4):375-82. Review. Abagyan R, Totrov M.

Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide. Biopolymers. 2001;60(2):124-33. Totrov M, Abagyan R.

In silico discovery of novel retinoic acid receptor agonist structures. BMC Struct Biol. 2001;1:1. Schapira M, Raaka BM, Samuels HH, Abagyan R.

Antibodies against thrombospondin-related anonymous protein do not inhibit Plasmodium sporozoite infectivity in vivo. Infect Immun. 2000 Jun;68(6):3667-73. Gantt S, Persson C, Rose K, Birkett AJ, Abagyan R, Nussenzweig V.

Genetic linkage mapping of zebrafish genes and ESTs. Genome Res. 2000 Apr;10(4):558-67. Kelly PD, Chu F, Woods IG, Ngo-Hazelett P, Cardozo T, Huang H, Kimm F, Liao L, Yan YL, Zhou Y, Johnson SL, Abagyan R, Schier AF, Postlethwait JH, Talbot WS.

Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition. J Mol Biol. 2000 Apr 21;298(1):95-110. Jin E, Katritch V, Olson WK, Kharatisvili M, Abagyan R, Pilch DS.

Expression of the adenovirus receptor and its interaction with the fiber knob. Exp Cell Res. 2000 Feb 25;255(1):47-55. Tomko RP, Johansson CB, Totrov M, Abagyan R, Frisén J, Philipson L.

Rational discovery of novel nuclear hormone receptor antagonists. Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1008-13. Schapira M, Raaka BM, Samuels HH, Abagyan R.

Estimating local backbone structural deviation in homology models. Comput Chem. 2000 Jan;24(1):13-31. Cardozo T, Batalov S, Abagyan R.

NRIF3 is a novel coactivator mediating functional specificity of nuclear hormone receptors. Mol Cell Biol. 1999 Oct;19(10):7191-202. Li D, Desai-Yajnik V, Lo E, Schapira M, Abagyan R, Samuels HH.

Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics. Structure. 1999 Jun 15;7(6):663-70. Stigler RD, Hoffmann B, Abagyan R, Schneider-Mergener J.

Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit. 1999 May-Jun;12(3):177-90. Review. Schapira M, Totrov M, Abagyan R.

A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res. 1999 Apr;9(4):334-47. Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D, Abagyan R, Schier AF, Talbot WS.

Identification of the individual residues that determine human CD59 species selective activity. J Biol Chem. 1999 Apr 16;274(16):10969-74. Zhang HF, Yu J, Chen S, Morgan BP, Abagyan R, Tomlinson S.

How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold Des. 1998;3(6):513-22. Zhou Y, Abagyan R.

Novel anchorage of GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP. Neuron. 1998 Sep;21(3):581-91. Srivastava S, Osten P, Vilim FS, Khatri L, Inman G, States B, Daly C, DeSouza S, Abagyan R, Valtschanoff JG, Weinberg RJ, Ziff EB.

Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast. EMBO J. 1998 Sep 15;17(18):5374-87. Isakoff SJ, Cardozo T, Andreev J, Li Z, Ferguson KM, Abagyan R, Lemmon MA, Aronheim A, Skolnik EY.

Energy strain in three-dimensional protein structures. Fold Des. 1998;3(4):259-69. Maiorov V, Abagyan R.

Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Sci. 1997 Oct;6(10):2143-58. Rashin AA, Rashin BH, Rashin A, Abagyan R.

Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity. Biochemistry. 1997 Aug 5;36(31):9423-8. Yu J, Dong S, Rushmere NK, Morgan BP, Abagyan R, Tomlinson S.

A new method for modeling large-scale rearrangements of protein domains. Proteins. 1997 Mar;27(3):410-24. Maiorov V, Abagyan R.

Mapping the active site of CD59. J Exp Med. 1997 Feb 17;185(4):745-53. Yu J, Abagyan R, Dong S, Gilbert A, Nussenzweig V, Tomlinson S.

Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins. 1997;Suppl 1:215-20. Totrov M, Abagyan R.

Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search. Proteins. 1997;Suppl 1:29-37. Abagyan R, Batalov S, Cardozo T, Totrov M, Webber J, Zhou Y.

Long pentraxins: an emerging group of proteins with diverse functions. Cytokine Growth Factor Rev. 1996 Aug;7(2):191-202. Review. Goodman AR, Cardozo T, Abagyan R, Altmeyer A, Wisniewski HG, Vilcek J.

The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J Mol Biol. 1996 Jul 26;260(4):588-603. Chalikian TV, Totrov M, Abagyan R, Breslauer KJ.

Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol. 1996 Mar;3(3):233-9. Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN.

The contour-buildup algorithm to calculate the analytical molecular surface. J Struct Biol. 1996 Jan-Feb;116(1):138-43. Totrov M, Abagyan R.

Homology modeling by the ICM method. Proteins. 1995 Nov;23(3):403-14. Cardozo T, Totrov M, Abagyan R.

Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8. Structure. 1995 Jul 15;3(7):669-79. Borchert TV, Kishan KV, Zeelen JP, Schliebs W, Thanki N, Abagyan R, Jaenicke R, Wierenga RK.

Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability. Protein Eng. 1995 Mar;8(3):249-59. Houbrechts A, Moreau B, Abagyan R, Mainfroid V, Préaux G, Lamproye A, Poncin A, Goormaghtigh E, Ruysschaert JM, Martial JA, et al.

The protein folding problem: finding a few minimums in a near infinite space. Comput Chem. 1994 Sep;18(3):225-31. Argos P, Abagyan R.

Recognition of distantly related proteins through energy calculations. Proteins. 1994 Jun;19(2):132-40. Abagyan R, Frishman D, Argos P.

Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol. 1994 Apr;1(4):259-63. Totrov M, Abagyan R.

Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1515-8. Borchert TV, Abagyan R, Jaenicke R, Wierenga RK.

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol. 1994 Jan 21;235(3):983-1002. Abagyan R, Totrov M.

The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. Structure. 1993 Nov 15;1(3):205-13. Borchert TV, Abagyan R, Kishan KV, Zeelen JP, Wierenga RK.

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. Eisenmenger F, Argos P, Abagyan R.

Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J Mol Biol. 1992 May 20;225(2):519-32. Abagyan R, Argos P.