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1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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


9. 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

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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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 , pdf

20. 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,

21. 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

22. 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


24. 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,

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 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 , pdf

34. 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

35. Cawston EE, Lam PC, Harikumar KG, Dong M, Ball AM, Augustine ML, Akgün E, Portoghese PS, Orry A, Abagyan R, Sexton PM, Miller LJ
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

36. 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

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

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

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

40. 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

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

42. 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 , pdf

43. 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 , pdf


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

45. 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

46. 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

47. 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 , pdf , supplement1

48. 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

49. 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 , pdf

50. 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 , pdf

51. 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 , pdf

52. 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 , pdf

53. 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

54. 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 , pdf

55. 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

56. 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 , pdf

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


58. 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 , pdf

59. 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,

60. 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 , pdf

61. 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 , pdf

62. 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 , pdf

63. 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

64. 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 , pdf

65. 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 , pdf

66. 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 , pdf

67. 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

68. 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 , pdf

69. 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 , pdf

70. 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 , pdf

71. 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 , pdf

72. 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 , pdf

73. 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


74. 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

75. 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

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

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

78. 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

79. 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

80. 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

81. 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

82. 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

83. 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

84. 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 , pdf

85. 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

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

87. 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

88. 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 , pdf


89. 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 , pdf

90. 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

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

92. 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

93. 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

94. 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

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

96. 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

97. 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 , pdf

98. 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

99. 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


100. 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

101. 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

102. 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

103. 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

104. 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

105. 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

106. 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 , pdf

107. 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

108. 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

109. 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

110. 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

111. 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

112. 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

113. 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

114. 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

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

116. 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


117. 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

118. 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

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

120. 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

121. 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

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

123. 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

124. 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

125. 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

126. 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


127. 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

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

129. 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

130. 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

131. 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

132. 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

133. 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

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

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

136. 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

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

138. 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


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

140. 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

141. 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

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

143. 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

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

145. 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

146. 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


147. 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

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

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

150. 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

151. 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

152. 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

153. 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

154. 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


155. 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

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

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

158. 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

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

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


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

162. 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

163. 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

164. 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


165. 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

166. 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

167. 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

168. 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

169. 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

170. 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

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


172. 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

173. 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

174. 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

175. 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

176. 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

177. 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

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

180. 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,


181. 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

182. 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

183. 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

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

185. 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


186. 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

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

188. 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

189. 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

190. 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

191. 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

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

193. 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

194. 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

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

196. 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


197. 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

198. 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

199. 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

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


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

202. 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

203. 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


204. 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

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

206. 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

207. 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 , pdf

208. 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

209. 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


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

211. 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

212. 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

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

214. 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

215. 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


216. 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


217. 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

218. 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

219. 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


220. 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

221. 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

222. 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


223. 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

224. 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

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


226. 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


227. 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


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

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


230. 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: 2014/07/21