Publications

Selected peer-reviewed publications by MolSoft's scientists, developers, and customers (from 2010 onwards) - ICM Methods and Applications

2011

Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A.
Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One. 2011;6(5):e18845 [NCBI_Abstract]

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(27):23888-99 [NCBI_Abstract]

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. Inherit Metab Dis. 2011 Jun;34(3):565-7. [NCBI_Abstract]

Monceaux CJ, Hirata-Fukae C, Lam PC, Totrov MM, Matsuoka Y, Carlier PR.
Triazole-linked reduced amide isosteres: An approach for the fragment-based drug discovery of anti-Alzheimer's BACE1 inhibitors. Bioorg Med Chem Lett. 2011 Jul 1;21(13):3992-6. [NCBI_Abstract]

Spurrier B, Sampson JM, Totrov M, Li H, O'Neal T, Williams C, Robinson J, Gorny MK, Zolla-Pazner S, Kong XP.
Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120. Structure. 2011 May 11;19(5):691-9. [NCBI_Abstract]

Benninghoff AD, Bisson WH, Koch DC, Ehresman DJ, Kolluri SK, Williams DE.
Estrogen-like activity of perfluoroalkyl acids in vivo and interaction with human and rainbow trout estrogen receptors in vitro. Toxicol Sci. 2011 Mar;120(1):42-58 [NCBI_Abstract]

Dey R, Chen L.
In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening. J Biomol Struct Dyn. 2011 Apr;28(5):695-715. [NCBI_Abstract]

Endsley MP, Hu Y, Deng Y, He X, Warejcka DJ, Twining SS, Gonias SL, Zhang M.
Maspin: the molecular bridge between the plasminogen activator system and {beta}1 integrin that facilitates cell adhesion. J Biol Chem. 2011 May 23. [NCBI_Abstract]

Pecic S, McAnuff MA, Harding WW.
Nantenine as an acetylcholinesterase inhibitor: SAR, enzyme kinetics and molecular modeling investigations.\ J Enzyme Inhib Med Chem. 2011 Feb;26(1):46-55. [NCBI_Abstract]

Chavez JD, Wu J, Bisson W, Maier CS.
Site-specific proteomic analysis of lipoxidation adducts in cardiac mitochondria reveals chemical diversity of 2-alkenal adduction. J Proteomics. 2011 Apr 13. [NCBI_Abstract]

Bahta M, Burke TR Jr.
Oxime-Based Click Chemistry in the Development of 3-Isoxazolecarboxylic Acid Containing Inhibitors of Yersinia pestis Protein Tyrosine Phosphatase, YopH. ChemMedChem. 2011 Jun 10. doi: 10.1002/cmdc.201100200. [NCBI_Abstract]

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(18):15895-907. [NCBI_Abstract]

Ungethüm L, Kenis H, Nicolaes GA, Autin L, Stoilova-McPhie S, Reutelingsperger CP.
Engineered annexin A5 variants have impaired cell entry for molecular imaging of apoptosis using pretargeting strategies. J Biol Chem. 2011 Jan 21;286(3):1903-10. [NCBI_Abstract]

Jubinsky PT, Short MK, Ghanem M, Das BC.
Design, synthesis, and biological activity of novel Magmas inhibitors. Bioorg Med Chem Lett. 2011 Jun 1;21(11):3479-82. [NCBI_Abstract]

Focher, Federico; Lossani, Andrea; Torti, Andrea; Gambino, Joseph; E. Wright, George
Binding Modes of 2-Phenylamino-6-oxopurines to Herpes Simplex Virus Thymidine Kinases Letters in Drug Design & Discovery, Volume 8, Number 1, January 2011 , pp. 1-8(8)

Bahta M, Lountos GT, Dyas B, Kim SE, Ulrich RG, Waugh DS, Burke TR Jr.
Utilization of nitrophenylphosphates and oxime-based ligation for the development of nanomolar affinity inhibitors of the Yersinia pestis outer protein H (YopH) phosphatase. J Med Chem. 2011 Apr 28;54(8):2933-43. [NCBI_Abstract]

Chan DS, Yang H, Kwan MH, Cheng Z, Lee P, Bai LP, Jiang ZH, Wong CY, Fong WF, Leung CH, Ma DL.
Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer. Biochimie. 2011 Jun;93(6):1055-64. [NCBI_Abstract]

Clement H, Odell G, Zamudio FZ, Redaelli E, Wanke E, Alagón A, Possani LD.
Isolation and characterization of a novel toxin from the venom of the spider Grammostola rosea that blocks sodium channels. Toxicon. 2007 Jul;50(1):65-74. [NCBI_Abstract]

Meli M, Gasset M, Colombo G.
Dynamic diagnosis of familial prion diseases supports the ¿2-¿2 loop as a universal interference target. PLoS One. 2011 Apr 28;6(4):e19093. [NCBI_Abstract]

Villoutreix BO, Laconde G, Lagorce D, Martineau P, Miteva MA, Dariavach P.
Tyrosine kinase syk non-enzymatic inhibitors and potential anti-allergic drug-like compounds discovered by virtual and in vitro screening. PLoS One. 2011;6(6):e21117. [NCBI_Abstract]

Yap DB, Chu J, Berg T, Schapira M, Cheng SW, Moradian A, Morin RD, Mungall AJ, Meissner B, Boyle M, Marquez VE, Marra MA, Gascoyne RD, Humphries RK, Arrowsmith CH, Morin GB, Aparicio SA.
Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood. 2011 Feb 24;117(8):2451-9. [NCBI_Abstract]

Ma DL, Chan DS, Lee P, Kwan MH, Leung CH.
Molecular modeling of drug-DNA interactions: Virtual screening to structure-based design. Biochimie. 2011 Apr 19. [NCBI_Abstract]

Belluti F, Bartolini M, Bottegoni G, Bisi A, Cavalli A, Andrisano V, Rampa A.
Benzophenone-based derivatives: a novel series of potent and selective dual inhibitors of acetylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation. Eur J Med Chem. 2011 May;46(5):1682-93. [NCBI_Abstract]

Leung CH, Chan DS, Kwan MH, Cheng Z, Wong CY, Zhu GY, Fong WF, Ma DL.
Structure-based repurposing of FDA-approved drugs as TNF-¿ inhibitors. ChemMedChem. 2011 May 2;6(5):765-8. [NCBI_Abstract]

Dong M, Le A, Te JA, Pinon DI, Bordner AJ, Miller LJ.
Importance of each residue within secretin for receptor binding and biological activity. Biochemistry. 2011 Apr 12;50(14):2983-93. [NCBI_Abstract]

Totrov M.
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S35 [NCBI_Abstract]

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(2):477-98. [NCBI_Abstract]

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 [NCBI_Abstract]

2010

Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S.
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology. 2010 Sep 30;405(2):513-23. [NCBI_Abstract]

Jiang X, Burke V, Totrov M, Williams C, Cardozo T, Gorny MK, Zolla-Pazner S, Kong XP.
Conserved structural elements in the V3 crown of HIV-1 gp120.
Nat Struct Mol Biol. 2010 Aug;17(8):955-61. [NCBI_Abstract]

Grigoryan AV, Kufareva I, Totrov M, Abagyan RA.
Spatial chemical distance based on atomic property fields.
J Comput Aided Mol Des. 2010 Mar;24(3):173-82. [NCBI_Abstract]

Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL.
Structure-Based Discovery of Natural-Product-like TNF-alpha Inhibitors.
Angew Chem Int Ed Engl 49, 2860-2864 (2010). [NCBI_Abstract]

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.
Chemistry & Biology 17, 471-482 (2010). [NCBI_Abstract]

Wang H, Blais J, Ron D, Cardozo T.
Structural Determinants of PERK Inhibitor Potency and Selectivity.
Chemical Biology & Drug Design 2010;76(6):480-495. [NCBI_Abstract]

Bai Y, Watt B, Wahome PG, Mantis NJ, Robertus JD.
Identification of new classes of ricin toxin inhibitors by virtual screening.
Toxicon 2010 Sep;56(4):526-534. [NCBI_Abstract]

Endo S, Matsunaga T, Kuwata K, Zhao H, El-Kabbani O, Kitade Y, Hara A.
Chromene-3-carboxamide derivatives discovered from virtual screening as potent inhibitors of the tumour maker, AKR1B10.
Bioorg. Med. Chem 2010 Apr;18(7):2485-2490. [NCBI_Abstract]

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 Jul 22;53(14):5267-80. 2010 [NCBI_Abstract]

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(47):13008-21. [NCBI_Abstract]

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(1):329-37. [NCBI_Abstract]

Rueda M, Bottegoni G, Abagyan R.
Recipes for the selection of experimental protein conformations for virtual screening.
J Chem Inf Model. 2010 Jan;50(1):186-93. [NCBI_Abstract]

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(1):197-211. [NCBI_Abstract]

Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R.
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists.
J Med Chem. 2010 Feb 25;53(4):1799-809. [NCBI_Abstract]

Dong M, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ.
Secretin occupies a single protomer of the homo-dimeric secretin receptor complex. Insights from photoaffinity labeling studies using dual sites of covalent attachment.
J Biol Chem 26;285(13):9919-31. 2010. [NCBI_Abstract]

Larsen CA, Dashwood RH, Bisson WH.
Tea catechins as inhibitors of receptor tyrosine kinases: mechanistic insights and human relevance.
Pharmacol Res. 2010 Dec;62(6):457-64. Epub 2010 Aug 4. [NCBI_Abstract]

O'Donnell EF, Saili KS, Koch DC, Kopparapu PR, Farrer D, Bisson WH, Mathew LK, Sengupta S, Kerkvliet NI, Tanguay RL, Kolluri SK.
The anti-inflammatory drug leflunomide is an agonist of the aryl hydrocarbon receptor.
PLoS One. 2010 Oct 1;5(10). [NCBI_Abstract]

Chavez JD, Bisson WH, Maier CS.
A targeted mass spectrometry-based approach for the identification and characterization of proteins containing a-aminoadipic and ?-glutamic semialdehyde residues.
Anal Bioanal Chem. 2010 Dec;398(7-8):2905-14. [NCBI_Abstract]

2009

Khan MTH, Fuskevåg O, Sylte I.
Discovery of potent thermolysin inhibitors using structure based virtual screening and binding assays.
J. Med. Chem 2009 Jan;52(1):48-61. [NCBI_Abstract]

Wu S, Bottini M, Rickert RC, Mustelin T, Tautz L.
In silico screening for PTPN22 inhibitors: active hits from an inactive phosphatase conformation.
ChemMedChem 2009 Mar;4(3):440-444. [NCBI_Abstract]

An J, Lee DC, Law AH, Yang CL, Poon LL, Lau AS, Jones SJ.
A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through Computational Screening against the Neuraminidase.
Journal of Medicinal Chemistry 52, 2667-2672 (2009). [NCBI_Abstract]

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 52, 5635-5641 (2009). [NCBI_Abstract]

Raush E, Totrov M, Marsden BD, Abagyan R.
A new method for publishing three-dimensional content.
PLoS ONE 2009;4(10):e7394. [NCBI_Abstract]

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;4(10):e7675. [NCBI_Abstract]

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 Aug;22(4):307-318. [NCBI_Abstract]

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(3):716-725. [NCBI_Abstract]

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;48(23):5303-5312. [NCBI_Abstract]

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;52(2):397-406. [NCBI_Abstract]

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;25(19):2544-2551. [NCBI_Abstract]

Gao F, Harikumar KG, Dong M, Lam PC, Sexton PM, Christopoulos A, Bordner A, Abagyan R, Miller LJ.
Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor.
Mol. Pharmacol 2009 Aug;76(2):264-274. [NCBI_Abstract]

Simms J, Hall NE, Lam PHC, Miller LJ, Christopoulos A, Abagyan R, Sexton PM.
Homology modeling of GPCRs.
Methods Mol. Biol 2009;552:97-113. [NCBI_Abstract]

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(5):273-288. [NCBI_Abstract]

Wu Y, 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;284(19):13185-13192. [NCBI_Abstract]

Nicola G, Abagyan R.
Structure-based approaches to antibiotic drug discovery.
Curr Protoc Microbiol 2009 Feb;Chapter 17:Unit17.2. [NCBI_Abstract]

Abagyan R, Kufareva I.
The flexible pocketome engine for structural chemogenomics.
Methods Mol. Biol 2009;575:249-279. [NCBI_Abstract]

2008

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(5):311-325. [NCBI_Abstract]

Carlier PR, Anderson TD, Wong DM, Hsu DC, Hartsel J, Ma M, Wong EA, Choudhury R, Lam PC, Totrov MM, Bloomquist JR.
Towards a species-selective acetylcholinesterase inhibitor to control the mosquito vector of malaria, Anopheles gambiae.
Chem Biol Interact. 2008 Sep 25;175(1-3):368-75. [NCBI_Abstract]

Totrov M.
Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR.
Chem Biol Drug Des. 2008 Jan;71(1):15-27. [NCBI_Abstract]

Kovacs JA, Yeager M, Abagyan R.
Damped-dynamics flexible fitting.
Biophys. J 2008 Oct;95(7):3192-3207. [NCBI_Abstract]

Ma D, Lai T, Chan F, Chung W, Abagyan R, Leung Y, Wong K.
Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking.
ChemMedChem 2008 Jun;3(6):881-884. [NCBI_Abstract]

Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J. D<
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins 2008 Aug;72(3):848-862. [NCBI_Abstract]

Bisson WH, Abagyan R, Cavasotto CN.
Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations.
J. Mol. Graph. Model 2008 Nov;27(4):452-458. [NCBI_Abstract]

Totrov M, Abagyan R.
Flexible ligand docking to multiple receptor conformations: a practical alternative.
Curr. Opin. Struct. Biol 2008 Apr;18(2):178-184. [NCBI_Abstract]

Nicola G, Smith CA, Abagyan R.
New method for the assessment of all drug-like pockets across a structural genome.
J. Comput. Biol 2008 Apr;15(3):231-240. [NCBI_Abstract]

Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S.
Optimization of high throughput virtual screening by combining shape-matching and docking methods.
J Chem Inf Model 2008 Mar;48(3):489-497. [NCBI_Abstract]

Dong M, Lam PC, Pinon DI, Sexton PM, Abagyan R, Miller LJ.
Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding.
Mol. Pharmacol 2008 Aug;74(2):413-422. [NCBI_Abstract]

Kufareva I, Abagyan R.
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states.
J. Med. Chem 2008 Dec;51(24):7921-7932. [NCBI_Abstract]

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 Jan 17; [Epub ahead of print] [NCBI_Abstract]

2007

Plewczynski D, Hoffmann M, von Grotthuss M, Ginalski K, Rychewski L.
In silico prediction of SARS protease inhibitors by virtual high throughput screening.
Chem Biol Drug Des 2007 Apr;69(4):269-279. [NCBI_Abstract]

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

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

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(22):5357-63. [NCBI_Abstract]

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(22):5330-8. [NCBI_Abstract]

Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, Pasquale EB, Kuhn P.
Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition.
J Biol Chem. 2007 Dec 14;282(50):36505-13. href="http://www.ncbi.nlm.nih.gov/pubmed/17897949">[NCBI_Abstract]

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(45):32834-43. [NCBI_Abstract]

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

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

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(3):686-91. [NCBI_Abstract]

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(2):280-90. [NCBI_Abstract]

Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R.
PIER: Protein interface recognition for structural proteomics.
Proteins. Feb13 Epub 2007 [NCBI_Abstract]

2006

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

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

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

Orry AJ, Abagyan RA, Cavasotto CN.
Structure-based development of target-specific compound libraries.
Drug Discov Today. 2006 Mar;11(5-6):261-6. [NCBI_Abstract]

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

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 Jan 4 [NCBI_Abstract]

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 Jan 11 [NCBI_Abstract]

2005

Cardozo T, Abagyan R.
Druggability of SCF Ubiquitin Ligase-Protein Interfaces.
Methods Enzymol. 2005;399:634-53. [NCBI_Abstract]

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(40):34073-9 [NCBI_Abstract]

Cavasotto, C.N., Orry, A.J.W., Abagyan R.
The challenge of considering receptor flexibility in ligand docking and virtual screening.
Curr. Comput. Aided Drug Des. 2005. 1, 423-440

Cavasotto CN, Kovacs JA, Abagyan RA.
Representing receptor flexibility in ligand docking through relevant normal modes.
J Am Chem Soc. 2005 Jul 6;127(26):9632-40. [NCBI_Abstract]

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

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

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

Cavasotto, C.N., Orry, A.J.W., Abagyan R.
Receptor Flexibility in Ligand Docking.
In Handbook of Theoretical and Computational Nanotechnology American Scientific. Publishers. Eds. Michael Rieth, Wolfram Schommers.

Fernandez-Recio, J., Totrov, M., Skorodumov, C., Abagyan, R.
Optimal Docking Area: A New Method for Predicting Protein-Protein Interaction Sites.
Proteins 57:400-13. [NCBI_Abstract]

2004

An, J., Totrov, M., Abagyan, R.
Comprehensive identification of "druggable" protein ligand binding sites.
Genome Inform Ser Workshop Genome Inform., 15(2):31-41. [NCBI_Abstract]

Bordner, A., and Abagyan, R.

Large-Scale Prediction of Protein Geometry and Stability Changes for Arbitrary Single-Point Mutations.
Proteins 57:400-13. [NCBI_Abstract]

Marsden, B., and Abagyan, R.
SAD - A normalized structural alignment database: improving sequence-structure alignments.
Bioinformatics, 20:2333-44. [NCBI_Abstract]

Cavasotto, C.N., Liu, G., James, S., Hobbs, P., Peterson, V., Bhattacharya, A., Kolluri, S., Zhang, X., Leid, M., Abagyan, R., Liddington, R., and Dawson, M.
Determinants of Retinoid X Receptor Transcriptional Antagonism
J. Med. Chem., 47:4360-72. [NCBI_Abstract]

Kovacs, J. Chacon, P., and Abagyan, R.
Predictions of Proteins Flexibility: First Order Measures.
Proteins, 56:661-8. [NCBI_Abstract]

Hill, T., Odell, L., Quan, A., Abagyan, R., Ferguson, G., Robinson, P., McCluskey, A.
Long Chain Amines and Long Chain Ammonium Salts as Novel Inhibitors of Dynamin GTPase Activity
Bioorganic Med Chem Letters Jun 21; 14(12): 3275-8 [NCBI_Abstract]

Fernandez-Recio, J., Totrov, M.M., and Abagyan, R.
Identification of Protein-Protein Interaction Sites From Docking Energy Landscapes

J. Mol. Biol. Jan 16; 335(3): 843-65. [NCBI_Abstract]

Cavasotto, C.N. and Abagyan, R.A.
Protein Flexibility in Ligand Docking and Virtual Screening To Protein Kinases
J. Mol. Biol. Mar 12; 337(1): 209-25 [NCBI_Abstract]

2003

Bordner, A.J., Cavasotto, C.N., and Abagyan, R.A.
Direct Derivation of Van der Waals Force Field Parameters From Quantum Mechanical Interaction Energies
J. Phys. Chem. B. 107: 9601-9609

Katritch, V., Totrov, M.M. and Abagyan, R.A.

Cavasotto, C., Orry, A.J.W., and Abagyan, R.A.
Structure-Based Identification of Binding Sites, Native Ligands and Potential Inhibitors for G-Protein Coupled Receptors
Proteins: Structure, Function, and Genetics 51(3), 423-433 [NCBI_Abstract]

Schapira, M.,Raaka, B., Das, S., Fan, L., Totrov, M., Zhou, Z., Wilson, S., Abagyan, R. and Samuels, H.
Discovery of Diverse Thyroid Hormone Receptor Antagonists by High-Throughput Docking

PNAS 100(12), 7354-7359 [NCBI_Abstract]

Fernandez-Recio, J., Totrov, M., and Abagyan, R.
ICM-DISCO Docking by Global Energy Optimization with Fully Flexible Side-Chains
Proteins 52:113-117 [NCBI_Abstract]

Schapira, M., Abagyan, R.A. and Totrov, M.M.
Nuclear Hormone Receptor Targeted Virtual Screening
J. Med. Chem. ASAP Article. 10.1021 [NCBI_Abstract]

Bursulaya, B., Totrov, M.M., Abagyan, R.A., and Brooks, C.
Comparative Study of Several Algorithms For Flexible Ligand Docking
J. Comp. Aided Mol. Design 17: 755-63 [NCBI_Abstract]

Marsden, B., and Abagyan, R.
Identifying Errors in Three-Dimensional Protein Models
Protein Structure: Determination, Analysis, and Applications for Drug Discovery, Daniel Chasman, Ed. Marcel Dekker, Inc. (Basel) 277-313 -

2002

Fernandez-Recio, J., Totrov, M.M., and Abagyan, R.A.
Soft Protein-Protein Docking in Internal Coordinates
Protein Science 11:280-91 [NCBI_Abstract]

Brive, L, and Abagyan, R.A.
Computational Structural Proteomics
Ernst Schering Res Found Workshop (38): 149-66 (Berlin) [NCBI_Abstract]

Schapira, M., Abagyan, R.A. and Totrov, M.M.
Structural Model of Nicotinic Acetylcholine Receptor Isotypes Bound to Acetylcholine and Nicotine.
BMC Structural Biology Journal 2(1):1. [NCBI_Abstract]

Bordner, A.J.,Cavasotto,C.N. and Abagyan,R.A.
Accurate Transferable Model for Water, N-Octanol, and N-Hexadecane Solvation Free Energies
J. Phys. Chem. B. 106:11009

2001

Abagyan, R.A. and Totrov, M.M.

High-Throughput Docking for Lead Generation
Current Opinion in Chemical Biology Aug;5(4):375-82 [NCBI_Abstract]

Norledge, B.V., Lambeir, A.M., Abagyan, R.A., Rottmann, A., Fernandez, A.M., Filimonov, V., Peter, M.G., and Wierenga, R.K.
Modeling, Mutagenesis, and Structural Studies on the Fully Conserved Phosphateloop (Loop 8) of Triosephosphate Isomerase: Toward a New Substrate Specificity
Proteins Feb 15;42(3), 383-9 [NCBI_Abstract]

Schapira, M., Raaka, B.M., Samuels, H.H., and Abagyan, R.A.
In Silico Discovery of Novel Retinoic Acid Receptor Agonist Structures
BMC Structural Biology Journal 2001;1(1):1 [NCBI_Abstract]

Totrov, M.M., and Abagyan, R.A.
Protein-Ligand Docking as an Energy Optimization Problem

Drug-Receptor Thermodynamics: Introduction and Applications. Editor: R.B. Raffa John Wiley & Sons, RV, 603-624

Totrov, M.M., and Abagyan, R.A.
Rapid Boundary Element Solvation Electrostatics Calculations in Folding Simulations: Successful Folding of a 23-Residue Peptide
Biopolymers 2001;60(2):124-33 [NCBI_Abstract]

2000

Cardozo, T., Batalov, S., and Abagyan, R.A.
Estimating Local Backbone Structural Deviation in Homology Models
Computers & Chemistry Jan 24(1), 13-31 [NCBI_Abstract]

Filikov, A.V., Mohan, V., Vickers, T.A., Griffey, R.H., Cook, P.D., Abagyan, R.A., and James, T.L.
Identification of Ligands For HIV-1 TAR RNA Via Structure Based Virtual Screening
JCAMD Aug 14(6), 593-610 [NCBI_Abstract]

Gantt, S., Persson, C., Rose, K., Birkett, A.J., Abagyan, R.A. and Nussenzweig, V.
Antibodies Against Trap Do Not inhibit Plasmodium Sporozoite infectivity in Vivo

Infection and Immunity Jun; 68(6), 3667-3673 [NCBI_Abstract]

Jin, E., Katritch, V., Olson, W.K., Kharatisvili, M., Abagyan, R.A., and Pilch, D.S.
Aminoglycoside Binding in The Major Groove of Duplex RNA: The Thermodynamic and Electrostatic Forces that Govern Recognition
J. Mol. Biol. Apr 21 298 (1), 95-110 [NCBI_Abstract]

Kelly, P.D., Chu, F., Wood, I.G., Ngo-Hazelett, P., Cardozo, T., Huang, H., Kimm, F., Liao, L., Yan, Y.L., Zhou, Y., Johnson, S.L., Abagyan, R.A., Schier, A.F., Postlethwait, J.H. and Talbot, W.S.
Genetic Linkage Mapping of Zebrafish Genes and ESTs
Genome Res Apr. 10 (4), 558-567 [NCBI_Abstract]

Schapira, M., Raaka, B.M., Samuels, H, H. and Abagyan, R.A.
Rational Discovery of Novel Nuclear Hormone Receptor Antagonists

PNAS Feb 1;97 (3), 1008-1013 [NCBI_Abstract]

Tomko, R.P., Totrov, M.M., Abagyan, R.A. and Philipson, L.
Expression of the Adenovirus Receptor and its Interaction with the Fiber Knob
Experimental Cell Research Feb 25;255(1), 47-55 [NCBI_Abstract]

1999

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

Gates, M., Kim, L., Egan, E., Cardozo, T., Sirotkin, H., Dougan, S., Lashkari, D., Davis, R., Abagyan, R.A., Schier, A,. and Talbot, W.

An Integrated Genetic Linkage Map of the Zebrafish Genome
Genome Research 9, 334-47 [NCBI_Abstract]

Li, D., Desai-Yajnik, V., Lo, E., Schapira, M., Abagyan, R.A., and Samulels, H.H.
NRIF3 Is a Novel Co-Activator Mediating Functional Specificity of Nuclear Hormone Receptors
Molecular and Cellular Biology Oct, 19 (10), 7191-7202 [NCBI_Abstract]

Schapira, M., Totrov, M.M., and Abagyan, R.A.
Prediction of the Binding Energy for Small Molecules, Peptides and Proteins
J. of Molecular Recognition 12, 177-190 [NCBI_Abstract]

Stigler, R.-D., Hoffmann, B, Abagyan, R.A. and Schneider-Mergener, J.
Soft Docking an L and a D Peptide to an Anticholera Toxin Antibody Using Internal Coordinate Mechanics

Structure 7, 663-670 [NCBI_Abstract]

Totrov, M.M., and Abagyan R.A.
Derivation of Sensitive Discrimination Potential for Virtual Ligand Screening
Proceedings of the Third Annual Intl. Conf. on Comp. Mol. Bio. 312-320

Zhang, H-F., Yu, J., Chen, S., Morgan, B.P., Abagyan, R.A. and Tomlinson, S.
Identification of the Individual Residues that Determine Human Cd59 Species Selective Activity
J.Biol.Chem. 274, 10969-10974 [NCBI_Abstract]

Zhou, Y., and Abagyan, R.A.
Efficient Stochastic Global Optimization for Protein Structure Prediction

Rigidity Theory and Application (M.F. Thorpe & P.M. Duxbury eds.) 345-356

1998

Cardozo, T.J. and Abagyan, R.A.
Molecular Modeling of the Domain Shared Between CED-4 and its Mammalian Homologue APAF-1: A Structural Relationship to the G-Proteins
J. of Mol. Model. 4, 83-93

Patel, I.R., Attur, M.G., Patel, R.N., Stuchin, S.A., Abagyan, R.A., Abramson, S.B., and Amin, A.R.
TNF-A Convertase Enzyme From Human Arthritis-Affected Cartilage: Isolation of CDNA by Differential Display, Expression of the Active Enzyme, and Regulation of Tnf-A
J. of Immunology 160, 4570-4579 [NCBI_Abstract]

Maiorov, V. and Abagyan, R.A.
Energy Strain in Three-Dimensional Protein Structures

Folding & Design 3, 259-269 [NCBI_Abstract]

Isakoff, S.J., Cardozo, T., Andreev, J., Li, Z., Ferguson, K.M., Abagyan, R.A., Lemmon, M.A., Aronheim, A and Skolnik, E.Y.
Identification and Analysis of Ph Domain-Containing Targets of Phosphatidylinositol 3-Kinase Using a Novel In Vivo Assay in Yeast
Embo J. 17 (18), 5374-87 [NCBI_Abstract]

Zhou, Y. and Abagyan, R.A.
How and Why Phosphotyrosine-Containing Peptides Bind to the SH2 and PTB Domains
Folding and Design 3, 513-522 [NCBI_Abstract]

Srivastava, S., Osten, P., Vilim, F.S.,Khatri, L., Inman, G., States, B., Daly, C., DeSouza, S., Abagyan, R.A., Valtschanoff, J.G., Weinberg, R.J. and Ziff, E.B.
Novel Anchorage of Glur2/3 to the Postsynaptic Density by the AMPA Receptor-Binding Protein ABP

Neuron 21, 581-591 [NCBI_Abstract]

1997

Thanki, N., Zeelen, J.Ph., Mathieu, M., Jaenicke, R., Abagyan, R.A., Wierenga R.K., and Schliebs, W.
Protein Engineering With Monomeric Triosephosphate Isomerase (Monotim): The Modelling and Structure Verification of A Seven Residue Loop
Protein Eng. 10, 159-167 [NCBI_Abstract]

Maiorov, V.N., and Abagyan, R.A.
A New Method for Modeling Large-Scale Rearrangements of Protein Domains
Proteins 27, 410-424 [NCBI_Abstract]

Yu, J., Abagyan, R., Dong, S., Gilbert, A., Nusenzweig, V., and Tomlinson, S.
Mapping of the Active Site of CD59

J. Expt. Medicine 185, 745-754 [NCBI_Abstract]

Abagyan, R.A., and Batalov, S.V.
Do Aligned Sequences Share The Same Fold?
J. Mol. Biol. 273, 355-368 [NCBI_Abstract]

Abagyan, R., and Totrov, M.
Contact Area Difference (CAD): A Robust Measure to Evaluate Accuracy of Protein Models
J. Mol. Biol. 268, 678-285 [NCBI_Abstract]

Yu, J., Dong, S., Rushmere, N.K., Morgan, B.P., Abagyan, R.A., and Tomlinson, S.
Mapping The Regions of The Complement Inhibitor CD59 Responsible for its Species Selective Activity

Biochemistry 36, 9423-9428 [NCBI_Abstract]

Koonin, E.V. and Abagyan, R.A.
TSG101 May Be the Prototype of A Class of Dominant Negative Ubiquitin Regulators
Nature Genetics 16, 330-331 [NCBI_Abstract]

Abagyan, R.A., Batalov, S., Cardozo, T., Totrov, M., and Zhou, Y.
Homology Modeling With ICM: Deformation Zone Mapping and Improvements of Models Via Conformational Search
Proteins Supplement 1, 29-37 [NCBI_Abstract]

Totrov, M.M., and Abagyan, R.A.
Flexible Protein-Ligand Docking by Global Energy Optimization in Internal Coordinates

Proteins Supplement 1, 215-220 [NCBI_Abstract]

Abagyan, R.A.
Protein Structure Prediction by Global Energy Optimization
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (van Gunsteren, W.F., et al., eds.). 3, 363-394

Rashin, A.A., Rashin, B.H., Rashin A., and Abagyan, R.
Evaluating the Energetics of Empty Cavities and Internal Mutations in Proteins
Protein Science 6, 2143-2158 [NCBI_Abstract]

Mathieu, M., Modis, Y., Zeelen, J. Ph., Engel, C.K., Abagyan, R.A., Ahlberg, A., Rasmussen, B., Lamzin, V.S., Kunau W.H., and Wierenga, R.K.
The 1.8 Crystal Structure of the Dimeric Peroxisomal 3-Ketoacyl-Coa Thiolase of Saccharomyces Cerevisiae: Implications for Substrate Binding and Reaction Mechanism

J. Mol. Biol. 273, 714-728 [NCBI_Abstract]

1996

Totrov, M.M., and Abagyan, R.A.
The Contour-Buildup Algorithm To Calculate The Analytical Molecular Surface
J. Struct. Biol. 116, 138-143 [NCBI_Abstract]

Chalikian, T.V., Totrov, M.M., Abagyan, R.A., and Breslauer, K.J.
The Hydration of Globular Proteins As Derived From Volume and Compressibility Measurements: Cross Correlating Thermodynamic and Structural Data
J. Mol. Biol. 260, 588-603 [NCBI_Abstract]

Strynadka, N.C.J., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B.K., Kuntz, I.D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., Zimmerman, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M., and James, M.N.G.
Molecular Docking Programs Successfully Predict The Binding of A Beta-Lactamase inhibitory Protein To Tem-1 Beta-Lactamase

Nature Struct. Biol. 3, 233-239 [NCBI_Abstract]

Goodman, A.R., Cardozo, T., Abagyan, R.A., Altmeyer, A., Wisniewski, H.G., and Vilcek, J.
Long Pentraxins: An Emerging Group of Proteins With Diverse Functions
Cytokine & Growth Factor Reviews 7, 191-202 [NCBI_Abstract]

1995

Borchert, T.V., Kishan, K.V.R., Zeelen, J.Ph., Schliebs, W., Thanki, N., Abagyan, R.A., Jaenicke, R., and Wierenga, R.K.
Three New Crystal Structures of Point Mutation Variants of Monotim: Conformational Flexibility of Loop-1, Loop-4 and Loop-8
Structure 3, 669-679 [NCBI_Abstract]

Houbrechts, A., Moreau, B., Abagyan, R., Mainfroid, V., Preaux G., Lamproye, A., Poncin, A., Goormaghtigh, E., Ryusschaert, J.-M., Martial, J.A., and Goraj, K.

Second-Generation Octarellins: Two New De Novo (??)8 Polypeptides Designed For investigating The influence of ?-Residue Packing On The ?/? -Barrel Structure Stability
Protein Engineering 8, 249-259 [NCBI_Abstract]

Cardozo, T., Totrov, M., and Abagyan, R.
Homology Modeling By The Icm Method
Proteins: Structure, Function, and Genetics 403-414 [NCBI_Abstract]

1994

Abagyan, R.A., Frishman, D., and Argos, P.
Recognition of Distantly Related Proteins Through Energy Calculations
Proteins 19, 132-140 [NCBI_Abstract]

Argos, P. and Abagyan, R.A.

The Protein Folding Problem: Finding A Few Minimums in A Near infinite Space
Computers & Chemistry 18, 225-232 [Abs.] - [NCBI_Abstract]

Abagyan, R.A. and Totrov, M.M.
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations For Peptides and Proteins
J. Mol. Biol. 235, 983-1002 [NCBI_Abstract]

Borchert, T.V., Abagyan, R.A., Jaenicke, R., and Wierenga, R.K.
Design, Creation, and Characterization of A Stable, Monomeric Triosephosphate Isomerase
Proc. Natl. Acad. Sci. USA 91, 1515-1518 [NCBI_Abstract]

Totrov, M.M. and Abagyan, R.A.
Detailed Ab initio Prediction of Lysozyme-Antibody Complex With 1.6 Accuracy

Nature Structural Biology 1, 259-263 [NCBI_Abstract]

Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A.
Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation
J. Comp. Chem. 15, 488-506

Totrov, M.M. and Abagyan, R.A.
Efficient Parallelization of The Energy, Surface and Derivative Calculations For internal Coordinate Mechanics
J. Comp. Chem. 15, 1105-1112