3 Publications

3.1 Papers

3.1.3 Drug design & flexible docking

1994

32. Totrov, M.M., and Abagyan, R.A. (1994). Detailed ab initio prediction of lysozyme-antibody complex with 1.6 accuracy. Nature Structural Biology, 1, 259-263 [Abs.]

1996

40. 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. (1996). Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Struct. Biol., 3, 233-239 [Abs.]

1997

50. Totrov, M., and Abagyan, R. (1997). Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins, Supplement 1, 215-220 [Abs.]-[PDF]

1999

62. Li, D., Desai-Yajnik, V., Lo, E., Schapira, M., Abagyan, R., and Samulels, H.H. (1999). NRIF3 is a novel co-activator mediating functional specificity of nuclear hormone receptors. Molecular and Cellular Biology Oct, 19 (10), 7191-7202 [Abs.]-[PDF]

63. Schapira, M., Totrov, M., and Abagyan, R. (1999). Prediction of the binding energy for small molecules, peptides and proteins.} J. of Molecular Recognition, 12, 177-190 [Abs.]

64. Stigler, R.-D., Hoffmann, B, Abagyan, R. and Schneider-Mergener, J. (1999). Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics. Structure, 7, 663-670 [Abs.]-[PDF]

65. Totrov, M., and Abagyan R. (1999). Derivation of sensitive discrimination potential for virtual ligand screening. Proceedings of the Third Annual Intl. Conf. on Comp. Mol. Bio. 312-320 [Abs.]

2000

69. Filikov, A.V., Mohan, V., Vickers, T.A., Griffey, R.H., Cook, P.D., Abagyan, R.A., and James, T.L. (2000). Identification of Ligands for HIV-1 TAR RNA via Structure Based Virtual Screening. JCAMD. Aug 14(6), 593-610 [Abs.]

71. Jin, E., Katritch, V., Olson, W.K., Kharatisvili, M., Abagyan, R., Pilch, D.S. (2000). 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 [Abs.]-[PDF]

73. Schapira, M., Raaka, B.M., Samuels, H, H. and Abagyan, R. (2000). Rational discovery of novel nuclear hormone receptor antagonists. PNAS, Feb 1;97 (3), 1008-1013 [Abs.]-[PDF]

2001

75. Abagyan, R. and Totrov, M. (2001). High-throughput Docking for Lead Generation. Current Opinion in Chemical Biology. Aug;5(4):375-82 [Abs.]-[PDF]

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

78. Totrov, M., and Abagyan, R. (2001). Protein-ligand docking as an energy optimization problem. Drug-Receptor Thermodynamics: Introduction and Applications. Editor: R.B. Raffa, John Wiley & Sons, RV, 603-624 [Abs.]

		1994
	32.	Totrov, M.M., and Abagyan, R.A. (1994). Detailed ab initio prediction of lysozyme-antibody complex with 1.6 accuracy. Nature Structural Biology, 1, 259-263 [Abs.]
		1996
	40.	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. (1996). Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Struct. Biol., 3, 233-239 [Abs.]
		1997
	50.	Totrov, M., and Abagyan, R. (1997). Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins, Supplement 1, 215-220 [Abs.]-[PDF]
		1999
	62.	Li, D., Desai-Yajnik, V., Lo, E., Schapira, M., Abagyan, R., and Samulels, H.H. (1999). NRIF3 is a novel co-activator mediating functional specificity of nuclear hormone receptors. Molecular and Cellular Biology Oct, 19 (10), 7191-7202 [Abs.]-[PDF]
	63.	Schapira, M., Totrov, M., and Abagyan, R. (1999). Prediction of the binding energy for small molecules, peptides and proteins.} J. of Molecular Recognition, 12, 177-190 [Abs.]
	64.	Stigler, R.-D., Hoffmann, B, Abagyan, R. and Schneider-Mergener, J. (1999). Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics. Structure, 7, 663-670 [Abs.]-[PDF]
	65.	Totrov, M., and Abagyan R. (1999). Derivation of sensitive discrimination potential for virtual ligand screening. Proceedings of the Third Annual Intl. Conf. on Comp. Mol. Bio. 312-320 [Abs.]
		2000
	69.	Filikov, A.V., Mohan, V., Vickers, T.A., Griffey, R.H., Cook, P.D., Abagyan, R.A., and James, T.L. (2000). Identification of Ligands for HIV-1 TAR RNA via Structure Based Virtual Screening. JCAMD. Aug 14(6), 593-610 [Abs.]
	71.	Jin, E., Katritch, V., Olson, W.K., Kharatisvili, M., Abagyan, R., Pilch, D.S. (2000). 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 [Abs.]-[PDF]
	73.	Schapira, M., Raaka, B.M., Samuels, H, H. and Abagyan, R. (2000). Rational discovery of novel nuclear hormone receptor antagonists. PNAS, Feb 1;97 (3), 1008-1013 [Abs.]-[PDF]
		2001
	75.	Abagyan, R. and Totrov, M. (2001). High-throughput Docking for Lead Generation. Current Opinion in Chemical Biology. Aug;5(4):375-82 [Abs.]-[PDF]
	77.	Schapira, M., Raaka, B. M., Samuels, H. H., and Abagyan, R. (2001). In Silico Discovery of novel Retinoic Acid Receptor Agonist Structures. BMC Structural Biology Journal 2001;1(1):1 [Abs.]-[PDF]
	78.	Totrov, M., and Abagyan, R. (2001). Protein-ligand docking as an energy optimization problem. Drug-Receptor Thermodynamics: Introduction and Applications. Editor: R.B. Raffa, John Wiley & Sons, RV, 603-624 [Abs.]