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2014

1. 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 5, 22, 1120-39, 25066135, PMC4126895

2. 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 α
Toxicol Sci, 2014 Jun 13, 24928891,

3. 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 Aug 14, 25051095,

4. 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, e97514, 24824618, PMC4019636

5. 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, 933-43, 24521202, PMC3982395

6. 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, e81454, 24489642, PMC3904831

7. 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, 717-23, 24406170, PMC3975830

8. 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 Feb 4, 48, 1964-72, 24392850, PMC3951377

9. 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, 301-9, 24217444, PMC3913357

10. 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, 554-64, 24344993,

2013

11. 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, 24330655, PMC3924234

12. Abagyan R, Ricci CG
The Human Pocketome
In: De novo Molecular Design, Ed. Gisbert Schneider, Wiley-VCH, 2013, 1, 79-96, ,

13. 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, 24034446, PMC3848485

14. 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, 794-807, 24021214, PMC3834142

15. 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, 2131-40, 23848971,

16. 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, 21082-95, 23754289, PMC3774375

17. 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, 364-73, 23664863, PMC4129370

18. 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, 23625495, PMC4091634

19. Vařeková RS, Geidl S, Ionescu CM, Skřehota O, Bouchal T, Sehnal D, Abagyan R, Koča J
Predicting p Ka values from EEM atomic charges.
J Cheminform, 2013 Apr 10, 5, 18, 23574978, PMC3663834

20. Gabrielsen M, Wołosewicz K, Zawadzka A, Kossakowski J, Nowak G, Wolak M, Stachowicz K, Siwek A, Ravna AW, Kufareva I, Kozerski L, Bednarek E, Sitkowski J, Bocian W, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z
Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors.
Chem Biol Drug Des, 2013 Jun, 81, 695-706, 23574807, PMC3665732

21. 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, e56150, 23437089, PMC3577790 , pdf

22. Schug, Abagyan, Blumberg, Collins, Crews, DeFur, Dickerson, Edwards, Gore, Guilette, Hayes, Heindel, Moores,Patisaul, Tal, Thayer, Vanderberg, Warner, Watson, vom Saal, Zoeller, O'Brien, Myers
Designing endocrine disruption out of the next generation of chemicals
Green Chem., 2013, 15, 181-198, ,

23. 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, 23092247, PMC4074518

24. Stevens RC, Cherezov V, Katritch V, Abagyan R, Kuhn P, Rosen H, Wüthrich K
The GPCR Network: a large-scale collaboration to determine human GPCR structure and function.
Nat Rev Drug Discov, 2013 Jan, 12, 25-34, 23237917, PMC3723354

2012

26. Abagyan R., Chen Y-C., Kufareva I.
Chapter 5. Docking, Screening and Selectivity Prediction for Small-molecule Nuclear Receptor Modulators
In: Computational Approaches to Nuclear Receptors, Eds. Cozzini P., Kellogg G., RSC Publishing, 2012, ISBN: 978-1-84973-535-3, 84-109, ,

28. 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, 1869-82, 23116466, PMC4085113

29. 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, 2705-14, 22947092, PMC3478405

30. 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, 5092-105, 22964305, PMC3509059

31. 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, 7998-8006, 22954387, PMC3474531

32. Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DS, Ma VP, Abagyan R, Wong CY, Ma DL
A metal-based inhibitor of tumor necrosis factor-α.
Angew Chem Int Ed Engl, 2012 Sep 3, 51, 9010-4, 22807261,

33. 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, 675-86, 22569591, PMC3398187

34. Chan FY, Neves MA, Sun N, Tsang MW, Leung YC, Chan TH, Abagyan R, Wong KY
Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds.
J Chem Inf Model, 2012 May 25, 52, 1367-75, 22559726,

35. 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, 7006-13, 22497303, PMC3613333 , pdf

36. 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, 4297-308, 22486652, PMC3479662

37. 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, 18618-35, 22467877, PMC3365725

38. 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, 3049-57, 22380603, , pdf

39. Orry AJ, Abagyan R
Preparation and refinement of model protein-ligand complexes.
Methods Mol Biol, 2012, 857, 351-73, 22323230,

40. Kufareva I, Abagyan R
Methods of protein structure comparison.
Methods Mol Biol, 2012, 857, 231-57, 22323224, , pdf

41. Katritch V, Rueda M, Abagyan R
Ligand-guided receptor optimization.
Methods Mol Biol, 2012, 857, 189-205, 22323222,

42. Jarończyk M, Wołosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z
Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors.
Eur J Med Chem, 2012 Mar, 49, 200-10, 22309909, PMC3365592

43. Abagyan R
Computational chemistry in 25 years.
J Comput Aided Mol Des, 2012 Jan, 26, 9-10, 22160588, , pdf

44. Kufareva I, Ilatovskiy AV, Abagyan R
Pocketome: an encyclopedia of small-molecule binding sites in 4D.
Nucleic Acids Res, 2012 Jan, 40, D535-40, 22080553, PMC3245087 , pdf

45. 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, 24-37, 22071255, PMC3357065 , pdf

2011

46. Katritch V, Abagyan R
GPCR agonist binding revealed by modeling and crystallography.
Trends Pharmacol Sci, 2011 Nov, 32, 637-43, 21903279, PMC3200445 , pdf

47. Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P
Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration.
Sci Signal, 2011 Sep 27, 4, ra64, 21954290,

48. 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, 895-911, 21904908, , pdf

49. 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, 1108-26, 21827947, PMC3154726 , pdf , supplement1

50. 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, 1795-806, 21761919, , pdf

51. 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, 930-44, 21742260, PMC3134789 , pdf

52. 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, 65-70, 21697825, PMC3131495 , pdf

53. Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A
Systematic exploitation of multiple receptor conformations for virtual ligand screening.
PLoS One, 2011, 6, e18845, 21625529, PMC3098722 , pdf

54. Dong M, Lam PC, Pinon DI, Hosohata K, Orry A, Sexton PM, Abagyan R, Miller LJ
Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore.
J Biol Chem, 2011 Jul 8, 286, 23888-99, 21566140, PMC3129170 , pdf

55. 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, 565-7, 21509537,

56. Miller LJ, Chen Q, Lam PC, Pinon DI, Sexton PM, Abagyan R, Dong M
Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling.
J Biol Chem, 2011 May 6, 286, 15895-907, 21454562, PMC3091199 , pdf

57. Leung CH, Chan DS, Yang H, Abagyan R, Lee SM, Zhu GY, Fong WF, Ma DL
A natural product-like inhibitor of NEDD8-activating enzyme.
Chem Commun (Camb), 2011 Mar 7, 47, 2511-3, 21240405, , pdf

58. Arnautova YA, Abagyan RA, Totrov M
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.
Proteins, 2011 Feb, 79, 477-98, 21069716, PMC3057902 , pdf

59. Katritch V, Kufareva I, Abagyan R
Structure based prediction of subtype-selectivity for adenosine receptor antagonists.
Neuropharmacology, 2011 Jan, 60, 108-15, 20637786, PMC2980563 , pdf

2010

60. 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, 1066-71, 20929726, PMC3074590 , pdf

61. Reynolds, K., Katritch, V., Abagyan, R.
Structure and modeling of GPCRs: implications for drug discovery
In: GPCR Molecular Pharmacology and Drug Targeting: Shifting Paradigms and New Directions (ed. Gilchrist, A.), Wiley & Sons, 2010, 1, 385–433, ,

62. Rueda M, Katritch V, Raush E, Abagyan R
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.
Bioinformatics, 2010 Nov 1, 26, 2784-5, 20871105, PMC2981495 , pdf

63. 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, 11443-5, 20669948, PMC2923663 , pdf

64. 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, 513-23, 20663531, PMC2942080 , pdf

65. 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, 5267-80, 20575553, , pdf

66. 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, 471-82, 20534345, PMC2884008 , pdf

67. 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, 459-71, 20455005, PMC2881208 , pdf

68. 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, 3899-906, 20441222, PMC2874095 , pdf

69. Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL
Structure-based discovery of natural-product-like TNF-α inhibitors.
Angew Chem Int Ed Engl, 2010 Apr 6, 49, 2860-4, 20235259, , pdf

70. Grigoryan AV, Kufareva I, Totrov M, Abagyan RA
Spatial chemical distance based on atomic property fields.
J Comput Aided Mol Des, 2010 Mar, 24, 173-82, 20229197, PMC2858276 , pdf

71. 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, 9919-31, 20100828, PMC2843239 , pdf

72. 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, 1799-809, 20095623, PMC2826142 , pdf

73. Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex.
Proteins, 2010 Jan, 78, 197-211, 20063437, PMC2805832 , pdf

74. Rueda M, Bottegoni G, Abagyan R
Recipes for the selection of experimental protein conformations for virtual screening.
J Chem Inf Model, 2010 Jan, 50, 186-93, 20000587, PMC2811216 , pdf

75. Chow KH, Sun RW, Lam JB, Li CK, Xu A, Ma DL, Abagyan R, Wang Y, Che CM
A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway.
Cancer Res, 2010 Jan 1, 70, 329-37, 19996284,

2009

76. Wu P, Ma DL, Leung CH, Yan SC, Zhu N, Abagyan R, Che CM
Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression.
Chemistry, 2009 Dec 7, 15, 13008-21, 19876976,

77. 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, e7675, 19847312, PMC2762615

78. Raush E, Totrov M, Marsden BD, Abagyan R
A new method for publishing three-dimensional content.
PLoS One, 2009 Oct 20, 4, e7394, 19841676, PMC2754609 , pdf

79. Abagyan R, Kufareva I
The flexible pocketome engine for structural chemogenomics.
Methods Mol Biol, 2009, 575, 249-79, 19727619, PMC2975493 , pdf

80. 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, 5635-41, 19719119, PMC3289977

81. Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P
FRODOCK: a new approach for fast rotational protein-protein docking.
Bioinformatics, 2009 Oct 1, 25, 2544-51, 19620099, PMC2800348

82. Simms J, Hall NE, Lam PH, Miller LJ, Christopoulos A, Abagyan R, Sexton PM
Homology modeling of GPCRs.
Methods Mol Biol, 2009, 552, 97-113, 19513644,

83. 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, 5303-12, 19441839, PMC3443625

84. Rueda M, Bottegoni G, Abagyan R
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.
J Chem Inf Model, 2009 Mar, 49, 716-25, 19434904, PMC2891173

85. 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, 264-74, 19429716, PMC2713122

86. 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, 307-18, 19353579, PMC2693451 , pdf

87. Wu YW, Goody RS, Abagyan R, Alexandrov K
Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation.
J Biol Chem, 2009 May 8, 284, 13185-92, 19240028, PMC2676050

88. Nicola G, Abagyan R
Structure-based approaches to antibiotic drug discovery.
Curr Protoc Microbiol, 2009 Feb, Chapter 17, Unit17.2, 19235149,

89. Reynolds KA, Katritch V, Abagyan R
Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators.
J Comput Aided Mol Des, 2009 May, 23, 273-88, 19148767, PMC2667566

90. Bottegoni G, Kufareva I, Totrov M, Abagyan R
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.
J Med Chem, 2009 Jan 22, 52, 397-406, 19090659, PMC2662720 , pdf

2008

91. 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, 7921-32, 19053777, PMC2669721 , pdf

92. 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, 452-8, 18805032,

93. Kovacs JA, Yeager M, Abagyan R
Damped-dynamics flexible fitting.
Biophys J, 2008 Oct, 95, 3192-207, 18586844, PMC2547429

94. 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, 413-22, 18467541, PMC3879803

95. 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, 881-4, 18383062, , pdf

96. 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, 231-40, 18333758, PMC2660599

97. Totrov M, Abagyan R
Flexible ligand docking to multiple receptor conformations: a practical alternative.
Curr Opin Struct Biol, 2008 Apr, 18, 178-84, 18302984, PMC2396190 , pdf

98. 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, 489-97, 18302357, , pdf

99. Bottegoni G, Kufareva I, Totrov M, Abagyan R
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).
J Comput Aided Mol Des, 2008 May, 22, 311-25, 18273556, PMC2641994 , pdf

100. 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, 848-62, 18260112,

101. Cavasotto CN, Orry AJ, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O'Neill KA, Hine H, Burton MS, Voigt JH, Abagyan RA, Bayne ML, Monsma FJ Jr
Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening.
J Med Chem, 2008 Feb 14, 51, 581-8, 18198821,

2007

102. 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, 18619-24, 18003900, PMC2141826

103. 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, 549-58, 17960327,

104. Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA
De novo discovery of serotonin N-acetyltransferase inhibitors.
J Med Chem, 2007 Nov 1, 50, 5330-8, 17924613, PMC2531295

105. Mallya M, Phillips RL, Saldanha SA, Gooptu B, Brown SC, Termine DJ, Shirvani AM, Wu Y, Sifers RN, Abagyan R, Lomas DA
Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates.
J Med Chem, 2007 Nov 1, 50, 5357-63, 17918823, PMC2631427

106. 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, 36505-13, 17897949,

107. Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ
Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues.
J Biol Chem, 2007 Nov 9, 282, 32834-43, 17827151,

108. 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, 11927-32, 17606915, PMC1924583 , pdf

109. 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, 516-9, 17588900,

110. 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, 15-28, 17524457, PMC2819402

111. Nicola G, Smith CA, Lucumi E, Kuo MR, Karagyozov L, Fidock DA, Sacchettini JC, Abagyan R
Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening.
Biochem Biophys Res Commun, 2007 Jul 6, 358, 686-91, 17509532, PMC1987361

112. 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, 1010-5, 17497806,

113. 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, 1950-9, 17496035, PMC1959528

114. Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ
Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor.
Mol Pharmacol, 2007 Aug, 72, 280-90, 17475809,

115. 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, 4522-31, 17381074, PMC2580722

116. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R
PIER: protein interface recognition for structural proteomics.
Proteins, 2007 May 1, 67, 400-17, 17299750, , pdf

117. Garzón JI, Kovacs J, Abagyan R, Chacón P
DFprot: a webtool for predicting local chain deformability.
Bioinformatics, 2007 Apr 1, 23, 901-2, 17277334,

118. Garzón JI, Kovacs J, Abagyan R, Chacón P
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.
Bioinformatics, 2007 Feb 15, 23, 427-33, 17150992,

2006

119. 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, 8265-72, 17165815, PMC3435108

120. 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, e362, 17105344, PMC1618416

121. Budagyan L, Abagyan R
Weighted quality estimates in machine learning.
Bioinformatics, 2006 Nov 1, 22, 2597-603, 16935929,

122. 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, 765-70, 16873024,

123. Huang Y, Qiao F, Abagyan R, Hazard S, Tomlinson S
Defining the CD59-C9 binding interaction.
J Biol Chem, 2006 Sep 15, 281, 27398-404, 16844690,

124. Orry AJ, Abagyan RA, Cavasotto CN
Structure-based development of target-specific compound libraries.
Drug Discov Today, 2006 Mar, 11, 261-6, 16580603,

125. Bordner AJ, Abagyan R
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.
Proteins, 2006 May 15, 63, 512-26, 16470819, , pdf

126. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
Anal Chem, 2006 Feb 1, 78, 779-87, 16448051,

127. Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ
In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells.
Bioorg Med Chem Lett, 2006 Apr 1, 16, 1969-74, 16413185,

128. 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, 76-8, 16406633, , pdf

2005

129. 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, 747-51, 16404815,

130. Cardozo T, Abagyan R
Druggability of SCF ubiquitin ligase-protein interfaces.
Methods Enzymol, 2005, 399, 634-53, 16338386,

131. Hill T, Odell LR, Edwards JK, Graham ME, McGeachie AB, Rusak J, Quan A, Abagyan R, Scott JL, Robinson PJ, McCluskey A
Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins.
J Med Chem, 2005 Dec 1, 48, 7781-8, 16302817,

132. Tetko IV, Abagyan R, Oprea TI
Surrogate data--a secure way to share corporate data.
J Comput Aided Mol Des, 2005 Sep-Oct, 19, 749-64, 16267691,

133. Huang Y, Smith CA, Song H, Morgan BP, Abagyan R, Tomlinson S
Insights into the human CD59 complement binding interface toward engineering new therapeutics.
J Biol Chem, 2005 Oct 7, 280, 34073-9, 16079145,

134. Cavasotto CN, Kovacs JA, Abagyan RA
Representing receptor flexibility in ligand docking through relevant normal modes.
J Am Chem Soc, 2005 Jul 6, 127, 9632-40, 15984891,

135. Forino M, Johnson S, Wong TY, Rozanov DV, Savinov AY, Li W, Fattorusso R, Becattini B, Orry AJ, Jung D, Abagyan RA, Smith JW, Alibek K, Liddington RC, Strongin AY, Pellecchia M
Efficient synthetic inhibitors of anthrax lethal factor.
Proc Natl Acad Sci U S A, 2005 Jul 5, 102, 9499-504, 15983377, PMC1160517

136. Fernández-Recio J, Abagyan R, Totrov M
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
Proteins, 2005 Aug 1, 60, 308-13, 15981266,

137. Bordner AJ, Abagyan R
Statistical analysis and prediction of protein-protein interfaces.
Proteins, 2005 Aug 15, 60, 353-66, 15906321,

138. An J, Totrov M, Abagyan R
Pocketome via comprehensive identification and classification of ligand binding envelopes.
Mol Cell Proteomics, 2005 Jun, 4, 752-61, 15757999, , pdf

139. Bordner AJ, Abagyan R
REVCOM: a robust Bayesian method for evolutionary rate estimation.
Bioinformatics, 2005 May 15, 21, 2315-21, 15749694,

140. Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R
Optimal docking area: a new method for predicting protein-protein interaction sites.
Proteins, 2005 Jan 1, 58, 134-43, 15495260, , pdf

2004

141. An J, Totrov M, Abagyan R
Comprehensive identification of "druggable" protein ligand binding sites.
Genome Inform, 2004, 15, 31-41, 15706489,

142. Bordner AJ, Abagyan RA
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations.
Proteins, 2004 Nov 1, 57, 400-13, 15340927, , pdf

143. 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, 4360-72, 15317450,

144. Kovacs JA, Chacón P, Abagyan R
Predictions of protein flexibility: first-order measures.
Proteins, 2004 Sep 1, 56, 661-8, 15281119,

145. 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, 3275-8, 15149689,

146. Marsden B, Abagyan R
SAD--a normalized structural alignment database: improving sequence-structure alignments.
Bioinformatics, 2004 Oct 12, 20, 2333-44, 15087320,

147. Cavasotto CN, Abagyan RA
Protein flexibility in ligand docking and virtual screening to protein kinases.
J Mol Biol, 2004 Mar 12, 337, 209-25, 15001363,

148. Fernández-Recio J, Totrov M, Abagyan R
Identification of protein-protein interaction sites from docking energy landscapes.
J Mol Biol, 2004 Jan 16, 335, 843-65, 14687579,

2003

149. Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd
Comparative study of several algorithms for flexible ligand docking.
J Comput Aided Mol Des, 2003 Nov, 17, 755-63, 15072435,

150. Zhou Y, Abagyan R
Algorithms for high-density oligonucleotide array.
Curr Opin Drug Discov Devel, 2003 May, 6, 339-45, 12833666,

151. Schapira M, Abagyan R, Totrov M
Nuclear hormone receptor targeted virtual screening.
J Med Chem, 2003 Jul 3, 46, 3045-59, 12825943,

152. Fernández-Recio J, Totrov M, Abagyan R
ICM-DISCO docking by global energy optimization with fully flexible side-chains.
Proteins, 2003 Jul 1, 52, 113-7, 12784376,

153. 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, 7354-9, 12777627, PMC165879

154. Cavasotto CN, Orry AJ, Abagyan RA
Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors.
Proteins, 2003 May 15, 51, 423-33, 12696053, , pdf

155. Eneqvist T, Lundberg E, Nilsson L, Abagyan R, Sauer-Eriksson AE
The transthyretin-related protein family.
Eur J Biochem, 2003 Feb, 270, 518-32, 12542701,

156. 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, 254-65, 12497604, , pdf

2002

157. Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, Winzeler EA
Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum.
Science, 2002 Oct 4, 298, 216-8, 12364807,

158. Brive L, Abagyan R
Computational structural proteomics.
Ernst Schering Res Found Workshop, 2002, , 149-66, 12061000,

159. Fernandez-Recio J, Totrov M, Abagyan R
Screened charge electrostatic model in protein-protein docking simulations.
Pac Symp Biocomput, 2002, , 552-63, 11928507,

160. Schapira M, Abagyan R, Totrov M
Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine.
BMC Struct Biol, 2002, 2, 1, 11860617, PMC65631

161. Zhou Y, Abagyan R
Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis.
BMC Bioinformatics, 2002, 3, 3, 11835687, PMC65509

162. Fernández-Recio J, Totrov M, Abagyan R
Soft protein-protein docking in internal coordinates.
Protein Sci, 2002 Feb, 11, 280-91, 11790838, PMC2373434

2001

163. Abagyan R, Totrov M
High-throughput docking for lead generation.
Curr Opin Chem Biol, 2001 Aug, 5, 375-82, 11470599,

164. Totrov M, Abagyan R
Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.
Biopolymers, 2001, 60, 124-33, 11455546,

165. Schapira M, Raaka BM, Samuels HH, Abagyan R
In silico discovery of novel retinoic acid receptor agonist structures.
BMC Struct Biol, 2001, 1, 1, 11405897, PMC32304

166. Norledge BV, Lambeir AM, Abagyan RA, Rottmann A, Fernandez AM, Filimonov VV, Peter MG, Wierenga RK
Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.
Proteins, 2001 Feb 15, 42, 383-9, 11151009,

2000

167. Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.
J Comput Aided Mol Des, 2000 Aug, 14, 593-610, 10921774,

168. 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, 3667-73, 10816526, PMC97657

169. 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, 558-67, 10779498, PMC310859

170. 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, 95-110, 10756107,

171. 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, 47-55, 10666333,

172. Schapira M, Raaka BM, Samuels HH, Abagyan R
Rational discovery of novel nuclear hormone receptor antagonists.
Proc Natl Acad Sci U S A, 2000 Feb 1, 97, 1008-13, 10655475, PMC15503

173. Cardozo T, Batalov S, Abagyan R
Estimating local backbone structural deviation in homology models.
Comput Chem, 2000 Jan, 24, 13-31, 10642877,

1999

174. 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, 7191-202, 10490654, PMC84712

175. 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, 663-70, 10404595,

176. Schapira M, Totrov M, Abagyan R
Prediction of the binding energy for small molecules, peptides and proteins.
J Mol Recognit, 1999 May-Jun, 12, 177-90, 10398408,

177. 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, 334-47, 10207156,

178. 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, 10969-74, 10196177,

179. Abagyan, R., Totrov, M.
Ab Initio Folding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure
Journal of Computational Physics, 1999, 151, 402-421, , , pdf

181. Totrov, M., Abagyan, R.
Derivation of sensitive discrimination potential for virtual ligand screening
Proceedings of RECOMB99, Lyon, France, ACM, 1999, , 312-320, , , pdf

182. Zhou, Y., Abagyan, R.
Efficient stochastic global optimization for protein structure prediction
Book: Rigidity Theory and Applications, Edited by Thorpe and Duxbury, Kluwer Academic/Plenum Publishers, 1999, , 345-356, ,

1998

183. Zhou Y, Abagyan R
How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains.
Fold Des, 1998, 3, 513-22, 9889165, , pdf

184. 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, 581-91, 9768844,

185. 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, 5374-87, 9736615, PMC1170863

186. Maiorov V, Abagyan R
Energy strain in three-dimensional protein structures.
Fold Des, 1998, 3, 259-69, 9710569, , pdf

187. Patel IR, Attur MG, Patel RN, Stuchin SA, Abagyan RA, Abramson SB, Amin AR
TNF-alpha convertase enzyme from human arthritis-affected cartilage: isolation of cDNA by differential display, expression of the active enzyme, and regulation of TNF-alpha.
J Immunol, 1998 May 1, 160, 4570-9, 9574564,

1997

188. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK
The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism.
J Mol Biol, 1997 Oct 31, 273, 714-28, 9402066,

189. Abagyan RA, Batalov S
Do aligned sequences share the same fold?
J Mol Biol, 1997 Oct 17, 273, 355-68, 9367768, , pdf

190. Rashin AA, Rashin BH, Rashin A, Abagyan R
Evaluating the energetics of empty cavities and internal mutations in proteins.
Protein Sci, 1997 Oct, 6, 2143-58, 9336837, PMC2143572

191. Yu J, Dong S, Rushmere NK, Morgan BP, Abagyan R, Tomlinson S
Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity.
Biochemistry, 1997 Aug 5, 36, 9423-8, 9235986,

192. Koonin EV, Abagyan RA
TSG101 may be the prototype of a class of dominant negative ubiquitin regulators.
Nat Genet, 1997 Aug, 16, 330-1, 9241264,

193. Abagyan RA, Totrov MM
Contact area difference (CAD): a robust measure to evaluate accuracy of protein models.
J Mol Biol, 1997 May 9, 268, 678-85, 9171291, , pdf

194. Maiorov V, Abagyan R
A new method for modeling large-scale rearrangements of protein domains.
Proteins, 1997 Mar, 27, 410-24, 9094743,

195. 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, 745-53, 9034152, PMC2196154

196. Thanki N, Zeelen JP, Mathieu M, Jaenicke R, Abagyan RA, Wierenga RK, Schliebs W
Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop.
Protein Eng, 1997 Feb, 10, 159-67, 9089815,

197. Totrov M, Abagyan R
Flexible protein-ligand docking by global energy optimization in internal coordinates.
Proteins, 1997, Suppl 1, 215-20, 9485515, , pdf

198. 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, 9485492,

1996

199. 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, 191-202, 8899296,

200. 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, 588-603, 8759322,

201. 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, 233-9, 8605624,

202. Totrov M, Abagyan R
The contour-buildup algorithm to calculate the analytical molecular surface.
J Struct Biol, 1996 Jan-Feb, 116, 138-43, 8742735,

1995

203. Cardozo T, Totrov M, Abagyan R
Homology modeling by the ICM method.
Proteins, 1995 Nov, 23, 403-14, 8710833, , pdf

204. Borchert TV, Kishan KV, Zeelen JP, Schliebs W, Thanki N, Abagyan R, Jaenicke R, Wierenga RK
Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8.
Structure, 1995 Jul 15, 3, 669-79, 8591044,

205. 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, 249-59, 7479687,

1994

206. Argos P, Abagyan R
The protein folding problem: finding a few minimums in a near infinite space.
Comput Chem, 1994 Sep, 18, 225-31, 7952893,

207. Abagyan R, Frishman D, Argos P
Recognition of distantly related proteins through energy calculations.
Proteins, 1994 Jun, 19, 132-40, 8090707,

208. Totrov M, Abagyan R
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy.
Nat Struct Biol, 1994 Apr, 1, 259-63, 7656055, , pdf

209. 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, 1515-8, 8108439, PMC43190 , pdf

210. Abagyan, R.A., Totrov, M.M. & Kuznetsov, D.N.
ICM - a new method for protein modelling and design. Applications to docking and structure prediction from the distorted native conformation
J.Comp.Chem., 1994, 15, 488-506, , , pdf

211. Abagyan R, Totrov M
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.
J Mol Biol, 1994 Jan 21, 235, 983-1002, 8289329, , pdf

1993

212. Kuznetsov DA, Abagyan RA
A technique for identifying atoms from a screen image.
J Mol Graph, 1993 Dec, 11, 245-7, 8136327,

213. Borchert TV, Abagyan R, Kishan KV, Zeelen JP, Wierenga RK
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop.
Structure, 1993 Nov 15, 1, 205-13, 16100954,

214. Dorofeyev VE, Mazur AK
Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin.
J Biomol Struct Dyn, 1993 Aug, 11, 143-67, 8216941,

215. Abagyan RA
Towards protein folding by global energy optimization.
FEBS Lett, 1993 Jun 28, 325, 17-22, 8513887, , pdf

216. Eisenmenger F, Argos P, Abagyan R
A method to configure protein side-chains from the main-chain trace in homology modelling.
J Mol Biol, 1993 Jun 5, 231, 849-60, 8515455,

217. Gibson TJ, Thompson JD, Abagyan RA
Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins.
Protein Eng, 1993 Jan, 6, 41-50, 8433970,

1992

218. Abagyan R, Argos P
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins.
J Mol Biol, 1992 May 20, 225, 519-32, 1593634, , pdf

1990

219. Abagyan RA, Mironov VN, Chernov BK, Chuprina VP, Ulyanov AV
Electrophoretic behavior of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n and implications for a DNA bending model.
Nucleic Acids Res, 1990 Feb 25, 18, 989-92, 2315048, PMC330354

220. Gromova II, Buchman VL, Abagyan RA, Ulyanov AV, Bronstein IB
Sequence dependent modulating effect of camptothecin on the DNA-cleaving activity of the calf thymus type I topoisomerase.
Nucleic Acids Res, 1990 Feb 11, 18, 637-45, 2155407, PMC333473

221. Eisenhaber F, Tumanyan VG, Abagyan RA
Structure of the hydration shells of oligo(dA-dT).oligo(dA-dT) and oligo(dA).oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations.
Biopolymers, 1990, 30, 563-81, 2265229,

1989

222. Abagyan RA, Maiorov VN
An automatic search for similar spatial arrangements of alpha-helices and beta-strands in globular proteins.
J Biomol Struct Dyn, 1989 Jun, 6, 1045-60, 2818856,

223. Abagyan RA, Mazur AK
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles.
J Biomol Struct Dyn, 1989 Feb, 6, 833-45, 2619943, , pdf

224. Mazur AK, Abagyan RA
New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures.
J Biomol Struct Dyn, 1989 Feb, 6, 815-32, 2619942, , pdf

1988

225. Chuprina VP, Abagyan RA
Structural basis of stable bending in DNA containing An tracts. Different types of bending.
J Biomol Struct Dyn, 1988 Aug, 6, 121-38, 3271514,

226. Abagyan RA, Maiorov VN
A simple qualitative representation of polypeptide chain folds: comparison of protein tertiary structures.
J Biomol Struct Dyn, 1988 Jun, 5, 1267-79, 3271511,

227. Chuprina VP, Abagyan RA
Anomalous properties of adenine.thymine tracts.
Nature, 1988 Mar 10, 332, 117, 3347251,

1985

228. Ivanitskiĭ GR, Esipova NG, Abagyan RA, Shnol' SE
[Block improvement of the genetic text as a factor of acceleration of biological evolution].
Biofizika, 1985 May-Jun, 30, 418-21, 4027270,

1984

229. Abagyan RA, 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, 476-82, 6548632,

1983

230. Abagyan RA
[Arrangement of molecular packing of collagen in fibrils].
Biofizika, 1983 May-Jun, 28, 498-500, 6871272,

231. Abagyan RA
[Diffraction from the alternating helix].
Biofizika, 1983 May-Jun, 28, 388-92, 6871260,

1981

232. Rogulenkova VN, Abagyan RA, Tumanian VG, Esipova NG
[Diffraction effects on x-rays of the oligotripeptide (Gly-Pro-Pro)10, isomorphic to collagen].
Biofizika, 1981 Jul-Aug, 26, 734-6, 7284464,

Last updated: 2014/08/05