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References


  • Fernandez-Recio, J., Totrov, M., and Abagyan, R. (2002). Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput. 2002;:552-63
  • Fernandez-Recio, J., Totrov, M., and Abagyan, R. (2002). Soft Protein-Protein Docking in Internal Coordinates. Protein Science 11:280-91
  • 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.
  • Totrov, M., and Abagyan, R. (2001). Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide. Biopolymers 2001;60(2):124-33.
  • 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
  • Norledge, B.V., Lambeir, A.M., Abagyan, R.A., Rottmann, A., Fernandez, A.M., Filimonov, V., Peter, M.G., and Wierenga, R.K. (2001). 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
  • Abagyan, R. and Totrov, M. (2001). High-throughput Docking for Lead Generation. Current Opinion in Chemical Biology. Aug;5(4):375-82
  • Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL.(2000) Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J Comput Aided Mol Des. 14(6):593-610.
  • Tomko, R.P., Totrov, M., Abagyan, R. and Philipson, L. (2000). Expression of the Adenovirus Receptor and Its Interaction with the Fiber Knob. Experimental Cell Research, Feb 25;255(1), 47-55.
  • Schapira, M., Raaka, B.M., Samuels, H, H. and Abagyan, R. (2000). Rational design of novel nuclear hormone receptor antagonists. PNAS 97 (3), 1008-1013.
  • 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.
  • 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., Schier, A.F., Postlethwait, J.H., Talbot, W.S. (2000) Genetic linkage mapping of zebrafish genes and ESTs. Genome Res. Apr. 10 (4), 558-567.
  • Gantt, S., Persson, C., Rose, K., Birkett, A.J., Abagyan, A. and Nussenzweig, V. (2000) Antibodies against TRAP do not inhibit Plasmodium sporozoite infectivity in vivo. Infection and Immunity Jun; 68(6), 3667-3673.
  • 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.
  • Zhang HF, Yu J, Chen S, Morgan BP, Abagyan R, Tomlinson S. (1999) Identification of the individual residues that determine human CD59 species selective activity. J Biol Chem 1999 Apr 16;274(16):10969-74
  • Schapira, M., Totrov, M. and Abagyan, R. Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit 12, 177-190 (1999).
  • Li, D., Desai-Yajnik, V., Lo, E., Schapira, M., Abagyan, R. and Samuels, H.H. NRIF3 Is a Novel Coactivator Mediating Functional Specificity of Nuclear Hormone Receptors. Mol Cell Biol 19, 7191-7202 (1999) .
  • Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D, Abagyan R, Schier AF, Talbot WSA. (1999) A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res 1999 Apr;9(4):334-47
  • Zhou Y, Abagyan R. (1999) Efficient Stochastic Global Optimization for Protein Structure Prediction. Rigidity Theory and Applications, Plenum Publishing, New York, 513-522.
  • Zhou Y, Abagyan R. (1998) How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Folding & Design., 3, 513-522.
  • Cardozo, T.J., Abagyan, R. (1998) Molecular Modeling of the Domain Shared Between CED-4 and its Mammalian Homologue Apaf-1: A Structural Relationship to the G-proteins. J. Mol. Model., 4, 83-93.
  • Maiorov, V. & Abagyan, R. (1998) Energy strain in three-dimensional protein structures Folding & Design., 3, 259-269.
  • Patel, I.R., Attur M.G., Patel R.N., Stuchin S.A., Abagyan R.A., Abramson S.B., Amin A.R. (1998) 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. 160, 4570-4579.
  • Srivastava S, Osten P, Vilim FS, Khatri L, Inman G, States B, Daly C, DeSouza S, Abagyan R, Valtschanoff JG, Weinberg RJ, Ziff EB., (1998) Novel anchorage of GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP. Neuron 21(3):581-91.
  • Totrov, M. & Abagyan, R. (1997) Flexible protein-ligand docking by global energy optimization in internal coordinates Proteins, Suppl. 1, 215-220 .
  • Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J. and Zhou, Y. (1997) Homology Modeling with Internal Coordinate Mechanics: Deformation Zone Mapping and Improvements of Models via Conformational Search. Proteins: Struct. Funct. & Gen., Suppl. 1, 29-37.
  • Abagyan, R.A. (1997) Protein structure prediction by global energy optimization. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Volume 3, Eds. van Gunsteren, W.F. et al., ESCOM Science Publishers BV, Leiden.
  • Mathieu, M., Modis, Y., Zeelen, J.P., Engel, C.K., Abagyan, R.A., Ahlberg, A., Rasmussen, B., Lamzin, V.S., Kunau, W.H., Wierenga, R.K. (1997) The 1.8A crystall structure of the dimeric peroxisomal 3-ketoacyl-coA thiolase of Saccharomyces cerevisiae: inplications for substrate binding and reaction mechanism. J. Mol. Biol., 273, 714-728.
  • Rashin, A.A., Rashin, B.H., Rashin A., Abagyan, R. (1997) Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Science, 6, 2143-2158.
  • Koonin, E.V. & Abagyan, R.A. (1997) TSG101, a gene mutated in human breast cancer, encodes a ubiquitin-conjugating enzyme homolog with replaced active cysteine . Nature Genetics, 16, 330-331.
  • Yu J, Dong S, Rushmere NK, Morgan BP, Abagyan R, Tomlinson S., (1997) Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity. Biochemistry 36, 9423-9428.
  • Yu, J., Abagyan, R.A., Dong, S., Gilbert, A., Nussenzweig, V., Tomlinson, S. (1997) Mapping the active site of CD59 J. Exp. Med. 185, 745-753.
  • Abagyan R.A. & Batalov, S. (1997) Do aligned sequences share the same fold? J. Mol. Biol. 273, 355-368.
  • Abagyan, R.A. & Totrov, M.M. (1997) Contact Area Difference (CAD): A robust measure to evaluate accuracy of protein models. J. Mol. Biol. 286, 678-685.
  • N.Thanki, J.Ph.Zeelen, M. Mathieu, R.Jaenicke, R.A.Abagyan, R.K.Wierenga and W.Schliebs (1997) Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven residue loop. Protein Eng., 10, 159-167.
  • Maiorov, V.N., Abagyan, R.A. (1997) A new method for modeling large-scale rearrangements of protein domains. Proteins 27, 410-424.
  • Strynadka, N.C., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B.K., Kuntz, I.D., Abagyan, R.A., Totrov, M., Janin, J., Cherfils, J., Zimmerman, F., Olson A., Duncan, B., Rao, M., Jackson, R. Sternberg, M., James, M.N. (1996) Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat. Struct. Biol., 3, 233-239.
  • Chalikian, T.V., Totrov, M.M., Abagyan, R.A., Breslauer, K.J. (1996) The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J. Mol. Biol. , 260, 588-603.
  • Totrov, M.M., and Abagyan, R.A. (1996) The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol., 115, 1-6.
  • Borchert, T.V., Kishan, K.V., Zeelen, J.P., Schliebs, W., Thanki, N., Abagyan, R., Jaenicke, R. & Wierenga, R.K. (1995) Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8. Structure, 3, 669-679.
  • Cardozo, T., Totrov, M.M. & Abagyan, R.A (1995) Homology modeling by the ICM method. Proteins, 23, 403-414.
  • Abagyan, R.A., Frishman, D., & Argos, P. (1994) Recognition of distantly related proteins through energy calculations. Proteins 19, 132-140.
  • Abagyan, R.A. & Totrov, M.M. (1994) Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235, 983-1002.
  • Abagyan, R.A., Totrov, M.M. & Kuznetsov, D.N. (1994) ICM - a new method for protein modelling and design. Applications to docking and structure prediction from the distorted native conformation. J.Comp.Chem. 15, 488-506.
  • Borchert, T.V., Abagyan, R.A., Jaenicke, R., & Wierenga, R.K. (1994) Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc. Natl. Acad. Sci USA 91, 1515-1518.
  • Totrov, M.M. & Abagyan, R.A. (1994) Efficient parallelization of the energy, surface and derivative calculations for internal coordinate mechanics. J. Comp. Chem 15, 1105-1112.
  • Totrov, M.M. & Abagyan, R.A. (1994) Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat. Struct. Biol. 1, 259-263.
  • Abagyan, R.A. (1993) Towards protein folding by global energy optimization. FEBS Letters 325, 17-22.
  • Borchert, T.V., Abagyan, R.A., Kishan, K.V.R., Zeelen, J.Ph., & Wierenga, R.K. (1994) The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. Structure 1, 205-213.
  • Eisenmenger, F., Argos, P., & Abagyan, R.A. (1993) A method to configure protein side-chains from the main-chain trace in homology modelling. J. Mol. Biol. 231, 849-860.
  • Abagyan, R.A. & Argos, P. (1992) Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J. Mol. Biol. 225, 519-532.

  • Abagyan, R.A. and Totrov, M.M. (1994). Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235, 983-1002.
  • Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.N. (1994). 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.

Other related publications
  • Abagyan, R.A. and Maiorov, V.N. (1988). A simple quantitative representation of polypeptide chain folds: comparison of protein tertiary structures. J. Biomol. Struct. Dyn. 5, 1267-1279.
  • Abagyan, R.A. and Mazur, A.K. (1989). New methodology for computer-aided modeling of biomolecular structure and dynamics. 2. Local deformations and cycles. J. Biomol. Struct. Dyn. 6, 833-845.
  • Abagyan, R.A. and Argos, P. (1992). Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J. Mol. Biol. 225, 519-532.
  • Borchert, T.V., Abagyan, R.A., Kishan, K.V.R., Zeelen, J.Ph., & Wierenga, R.K. (1994). The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modeling of an eight-residue loop. Structure 1, 205-213.
  • Borchert, T.V., Abagyan, R.A., Jaenicke, R., and Wierenga, R.K. (1994). Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc. Natl. Acad. Sci USA 91, 1515-1518.
  • Eisenmenger, F., Argos, P., and Abagyan,R.A. (1993). A method to configure protein side-chains from the main-chain trace in homology modeling. J. Mol. Biol. 231, 849-860.
  • Mazur, A.K. and Abagyan, R.A. (1989). New methodology for computer-aided modeling of biomolecular structure and dynamics. 1. Non-cyclic structures. J. Biomol. Struct. Dyn. 6, 815-832.
  • Totrov, M.M. and Abagyan, R.A. (1994). Efficient parallelization of the energy, surface and derivative calculations for internal coordinate mechanics. J. Comp. Chem 15, 1105-1112.
  • Totrov, M.M. and Abagyan, R.A. (1994). Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nature Struct. Biol. 1, 259-263.
  • Totrov, M.M., and Abagyan, R.A. (1996). The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 115, 1-6.
  • Abagyan, R.A., and Batalov, S. (1997) Do aligned sequences share the same fold? J. Mol. Biol., 273, 1, 355-368.
  • Abagyan, R. and Totrov, M. (1997) Contact Area Difference (CAD): A robust measure to evaluate accuracy of protein models. J. Mol. Biol. 268, 678-285.

Applications of the ICM program
  • Cardozo, T., Totrov, M., and Abagyan, R. (1995) Homology modeling by the ICM method. Proteins 23, 403-414 .
  • Borchert, T.V., Kishan, K.V.R., Zeelen, J.Ph., Schliebs, W., Thanki, N., Abagyan, R.A., Jaenicke, R., and Wierenga, R.K. (1995 ) Three new crystal structures of point mutation variants of monoTIM: Conformational flexibility of loop-1, loop4 and loop8. Structure 3, 669-679.
  • 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.
  • Chalikian,T.V., Totrov, M.M., Abagyan, R.A., Breslauer, K.J. (1996) The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J. Mol. Biol. 260, 588-603.
  • Thanki, N., Zeelen, J.Ph., Mathieu, M., Jaenicke, R., Abagyan, R.A., Wierenga, R.K., and W.Schliebs (1997) Protein engineering with monomeric triosephosphate isomerase (monoTIM): The modeling and structure verification of a seven residue loop. Protein Eng. 10, 159-167.
  • Goodman, A.R., Cardozo, T., Abagyan, R.A., Altmeyer, A., Wisniewski, H.G., and Vilcek, J. (1996) Long pentraxins: an emerging group of proteins with diverse functions. Cytokine Growth Factor Rev. 7, 191-202.
  • Maiorov, V.N. and Abagyan, R.A. (1997) A new method for modeling large-scale rearrangements of protein domains. Proteins 27, 410-424.
  • Yu, J., Abagyan, R., Dong, S., Gilbert, A., Nusenzweig, V., & Tomlinson, S. (1997) Mapping of the Active Site of CD59. J. Expt. Medicine 185, 745-754.

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