2013

1. 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

2. Svobodová Va Eková R, Geidl S, Ionescu CM, Sk Ehota OE, Bouchal T, Sehnal D, Abagyan R, Koca J
Predicting pKa values from EEM atomic charges.
J Cheminform, 2013 Apr 10, 5, 18, 23574978

3. 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 Apr 11, 23574807

4. 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

5. 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,

2012

9. 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,

13. 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

14. 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

15. 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

17. 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

19. 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

20. 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

21. 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

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

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

25. 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

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

28. 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

2011

30. 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

34. 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

35. 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

37. 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

38. 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

39. 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

40. 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

41. 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

2010

45. 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,

46. 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

47. 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

49. 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

50. 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

53. 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

54. 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

55. 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

57. 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

58. 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

59. 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

60. 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

61. 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

64. 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

65. 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

66. 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

67. 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

68. 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

69. 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

71. 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

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

73. 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

2008

76. 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

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

78. 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

79. 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

80. 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

81. 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

82. 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

84. 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

85. 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

86. 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

87. 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

88. 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

89. 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

90. 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

91. 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

93. 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

94. 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

95. 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

96. 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

97. 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

98. 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

99. 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

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

102. 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

103. 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

104. 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

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

106. 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

107. 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

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

110. 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

111. 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

2005

113. 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

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

115. 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

116. 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

117. 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

118. 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

119. 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

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

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

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

2004

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

127. 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

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

129. 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

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

131. 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

132. 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

133. 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

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

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

136. 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

137. 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

139. 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

2002

141. 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

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

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

144. 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

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

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

2001

150. 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

151. 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

152. 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

153. 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

154. 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

155. 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

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

1999

158. 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

159. 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

160. 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

161. 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

162. 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