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3.1 Papers
Section Intro | Molecular modeling | Bioinformatics | docking | Methods and algorithms | Applications | Chronological list

Here you can find all the papers we have or have helped to write, arranged in chronological order. If you just want papers about a specific topic, please follow the links below to go to the subset of papers that better suits your interests.

The search engine (located at the left upper corner of this window) can be used to search for papers that contains the word(s) you enter as a query.

Every paper is linked to its abstract and/or PDF file (when available).

    1983
  1. Abagyan, R.A. (1983). Diffraction from a variable sign helix. Biophysics, 28, 388-392 [Abs.]
  2. Abagyan, R.A., Rogulenkova, V.N., Tumanyan, V.G., Esipova, N.G. (1983). Investigation of diffraction effects appearing on packing of helical molecules. Biophysics, 28, 897-904 [Abs.]
  3. Abagyan, R.A. (1983). Molecular arrangement in collagen fibrils. Biophysics, 28, 498-500 [Abs.]

    1984

  4. Abagyan, R.A., Tumanyan, V.G., Esipova, N.G. (1984). Two types of tripeptide conformations in collagen. Calculation of the (Gly-Pro-Ser)n and (Gly-Val-Hyp)n structures. Bioorganic Chemistry, 10, 476-482 [Abs.]
  5. Tumanyan, V.G., Abagyan, R.A., Esipova, N.G. (1984). Conformational analysis of polytripeptides (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n, and (Gly-Ala-Ala)n in connection with the problem of collagen structure. Biopolymers, 23, 1499-1512 [Abs.]

    1985

  6. Ivanitskii, G.R., Esipova, N.G., Abagyan, R.A., Shnol, S.E. (1985). Block improvement of the genetic text as a factor of acceleration of biological evolution. Biofizika, 30, 418-421 [Abs.]

    1988

  7. 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 [Abs.]
  8. Chuprina, V.P., Abagyan, R.A. (1988). Anomalous properties of adenine-thymine tracts. Nature, 332, 117 [Abs.]
  9. Chuprina, V.P., Abagyan, R.A. (1988). Structural Basis of Stable Bending of DNA Containing Oligo(dA) tracts. Different Types of Bending. J. Biomol. Struct. Dyn., 6, 121-138 [Abs.]

    1989

  10. Mazur, A.K., and Abagyan, R.A. (1989). New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics. 1. Non-Cyclic Structures. J. Biomol. Struct. Dyn., 6, 815-832 [Abs.]
  11. Abagyan, R.A., and Mazur, A.K. (1989). New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics. 2. Local Deformations and Cycles. J. Biomol. Struct. Dyn., 6, 833-845 [Abs.]
  12. Abagyan, R.A., and Maiorov, V.N. (1989). An Automatic Search for Similar Spatial Arrangements of ß-Helices and ß-Strands in Globular Proteins. J. Biomol. Struct. Dyn., 6, 1045-1060 [Abs.]
  13. Abagyan, R.A., and Ul'yanov, A.V. (1989). General Patterns of DNA Sequences in Regions of Interaction with Proteins. Doklady Academii Nauk SSSR, 304, 741-745 [Abs.]

    1990

  14. Abagyan, R.A., and Mazur, A.K. (1990). Conformational Energy Derivatives for Polypeptides with Flexible Proline Rings.} Computers & Chem., 14, 169-175 [Abs.]
  15. Abagyan, R.A., Mironov, V.N., Chernov, B.K., Chuprina, V.P., Ulyanov, A.V. (1990). Electrophoretic behaviour of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n and implications for a DNA bending model. Nucl. Acids Res., 18, 989-992 [Abs.]
  16. Eisenhaber, F., Tumanyan, V.G., Abagyan, R.A. (1990). 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, 30, 563-581 [Abs.]
  17. Gromova, I.I., Buchman, V.L., Abagyan, R.A., Ulyanov, A.V. and Bronstein, I.B. (1990). Sequence dependent modulating effects of camptothecin on the DNA cleaving activity of the calf thymus type I topoisomerase. Nucl. Acids Res., 18, 637-645 [Abs.]

    1991

  18. Mazur, A.K., Dorofeev, V.E., and Abagyan, R.A. (1991). Derivation and Testing of Explicit Equations of Motion for Polymers Described by Internal Coordinates. J. Comput. Phys., 92, 261-272 [Abs.]

    1992

  19. 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 [Abs.]
  20. Abagyan, R.A., Eisenmenger, F., and Argos, P. (1992). Techniques for conformational searches of peptides and proteins. Computer Aided Innovation of New Materials II (Doyama, M., Kihara, J., Tanaka, M., and Yamamoto, R., eds.), 2, 1241-1246 [Abs.]
  21. Abagyan, R.A., and Argos, P. (1992). Prediction of protein side-chain conformation by packing optimization. Chemtracts - BIochemistry and Molecular Biology, 2, 324-327 [Abs.]
  22. Petukhov, M.G., Dorofeev, V.E., Abagyan, R.A., Mazur, A.K. (1992). Global optimization of the conformational energy of oligopeptides using a tunnel algorithm. Biofizika, 37, 226-230 [Abs.]

    1993

  23. Abagyan, R.A. (1993). Towards protein folding by global energy optimization. FEBS Letters, 325,17-22 [Abs.]
  24. Borchert, T.V., Abagyan, R.A., Kishan, K.V. R., Zeelen, J.Ph., and Wierenga, R.K. (1993). The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modeling of an eight-residue loop. Structure, 1, 205-213 [Abs.]
  25. Eisenmenger, F., Argos, P., and Abagyan, R.A., (1993). A method to configure protein side-chains from the mainchain trace in homology modeling. J. Mol. Biol., 231, 849-860 [Abs.]
  26. Gibson, T.J., Thompson, J.D. and Abagyan, R.A (1993). Proposed structure for the DNA-binding Domain of the Helix-Loop-Helix family of eucaryotic gene regulatory proteins. Protein Engineering, 6, 41-50 [Abs.]
  27. Kuznetsov, D.A., and Abagyan, R.A. (1993). A technique for identifying atoms from a screen image. J. Mol. Graph., 11, 245-247 [Abs.]

    1994

  28. Abagyan, R.A., Frishman, D., and Argos, P. (1994). Recognition of distantly related proteins through energy calculations. Proteins, 19, 132-140 [Abs.]
  29. Argos, P., and Abagyan, R.A. (1994). The protein folding problem: finding a few minimums in a near infinite space. Computers & Chemistry, 18, 225-232 [Abs.]
  30. 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 [Abs.]-[PDF]
  31. 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 [Abs.]-[PDF]
  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.]
  33. Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A. (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 [Abs.]
  34. 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 [Abs.]

    1995

  35. 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, loop-4 and loop-8. Structure, 3, 669-679 [Abs.]-[PDF]
  36. Houbrechts, A., Moreau, B., Abagyan, R., Mainfroid, V., Preaux G., Lamproye, A., Poncin, A., Goormaghtigh, E., Ryusschaert, J.-M., Martial, J.A., Goraj, K. (1995). 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 [Abs.]
  37. Cardozo, T., Totrov, M., and Abagyan, R. (1995). Homology modeling by the ICM method. Proteins: Structure, Function, Genetics, 23, 403-414 [Abs.]

    1996

  38. Totrov, M.M., and Abagyan, R.A. (1996). The Contour-Buildup Algorithm to Calculate the Analytical Molecular Surface. J. Struct. Biol., 116, 138-143 [Abs.]-[PDF]
  39. 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 [Abs.]-[PDF]
  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.]
  41. 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 Reviews, 7, 191-202 [Abs.]

    1997

  42. Thanki, N., Zeelen, J.Ph., Mathieu, M., Jaenicke, R., Abagyan, R.A., Wierenga R.K., and Schliebs, W. (1997). Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven residue loop. Protein Eng., 10, 159-167 [Abs.]-[PDF]
  43. Maiorov, V.N., and Abagyan, R.A. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins, 27, 410-424 [Abs.]-[PDF]
  44. Yu, J., Abagyan, R., Dong, S., Gilbert, A., Nusenzweig, V., and Tomlinson, S. (1997). Mapping of the Active Site of CD59. J. Expt. Medicine, 185, 745-754 [Abs.]-[PDF]
  45. Abagyan, R.A., and Batalov, S.V. (1997). Do aligned sequences share the same fold? J. Mol. Biol., 273, 355-368 [Abs.]-[PDF]
  46. 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 [Abs.]-[PDF]
  47. Yu, J., Dong, S., Rushmere, N.K., Morgan, B.P., Abagyan, R., and Tomlinson, S. (1997). Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity. Biochemistry, 36, 9423-9428 [Abs.]-[PDF]
  48. Koonin, E.V., and Abagyan, R.A. (1997). TSG101 may be the prototype of a class of dominant negative ubiquitin regulators. Nature Genetics, 16, 330-331 [Abs.]
  49. Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., and Zhou, Y. (1997). Homology modeling with ICM: deformation zone mapping and improvements of models via conformational search. Proteins, Supplement 1, 29-37 [Abs.]-[PDF]
  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]
  51. Abagyan, R. (1997). 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 [Abs.]
  52. 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 [Abs.]

    1998

  53. 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. (1997). 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 [Abs.]-[PDF]
  54. Cardozo, T.J., and 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. of Mol. Model., 4, 83-93 [Abs.]
  55. Patel, I.R., Attur, M.G., Patel, R.N., Stuchin, S.A., Abagyan, R.A., Abramson, S.B., and Amin, A.R. (1998). 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 [Abs.]-[PDF]
  56. Maiorov, V., and Abagyan, R. (1998). Energy strain in three-dimensional protein structures. Folding & Design, 3, 259-269 [Abs.]-[PDF]
  57. Isakoff, S.J., Cardozo, T., Andreev, J., Li, Z., Ferguson, K.M., Abagyan, R., Lemmon, M.A., Aronheim, A and Skolnik, E.Y. (1998). 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 [Abs.]-[PDF]
  58. Zhou, Y. and Abagyan, R. (1998). How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Folding and Design, 3, 513-522 [Abs.]-[PDF]
  59. Srivastava, S., Osten, P., Vilim, F.S.,Khatri, L., Inman, G., States, B., Daly, C., DeSouza, S., Abagyan, R., Valtschanoff, J.G., Weinberg, R.J. & Ziff, E.B. (1998). Novel Anchorage of GluR2/3 to the Postsynaptic Density by the AMPA Receptor-Binding Protein ABP. Neuron 21, 581-591 [Abs.]-[PDF]

    1999

  60. Abagyan, R., and Totrov, M. (1999). Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. Journal of Computational Physics, 151, 402-421 [Abs.]-[PDF]
  61. Gates, M., Kim, L., Egan, E., Cardozo, T., Sirotkin, H., Dougan, S., Lashkari, D., Davis, R., Abagyan, R., Schier, A,. and Talbot, W. (1999). An integrated genetic linkage map of the zebrafish genome. Genome Research 9, 334-47 [Abs.]-[PDF]
  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.]
  66. Zhang, H-F., Yu, J., Chen, S., Morgan, B.P., Abagyan, R. and Tomlinson, S. (1999). Identification of the Individual Residues that Determine Human CD59 Species Selective Activity. J.Biol.Chem., 274, 10969-10974 [Abs.]-[PDF]
  67. Zhou, Y., and Abagyan, R. (1999). Efficient stochastic global optimization for protein structure prediction. Rigidity Theory and Application (M.F. Thorpe & P.M. Duxbury eds.), 345-356 [Abs.]

    2000

  68. Cardozo, T., Batalov, S., and Abagyan, R. (2000). Estimating local backbone structural deviation in homology models. Computers & Chemistry . Jan 24(1), 13-31 [Abs.]
  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.]-[PDF]
  70. 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 [Abs.]-[PDF]
  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]
  72. 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 [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]
  74. 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 [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]
  76. 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 [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.]
  79. 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 [Abs.]-[PDF]

    2002

  80. Fernandez-Recio, J., Totrov, M., and Abagyan, R. (2002). Soft Protein-Protein Docking in Internal Coordinates. Protein Science 11:280-91 [Abs.]-[PDF]
  81. Zhou, Y. and Abagyan, R. (2002). Match-Only Integral Distribution (MOID) Algorithm for High-Density Oligonucleotide Array Analysis. BMC Bioinformatics 3:3 [Abs.]-[PDF]
  82. Fernandez-Recio, J., Totrov, M., and Abagyan, R. (2002). Screened charge electrostatic model in protein-protein docking simulations. Pac Symp Biocomput. 2002;:552-63 [Abs.]-[PDF]
  83. Volkman, S.K., Hartl, D.L., Wirth, D.F., Nielsen, K.M., Choi, M., Le Roch, K.G., Abagyan, R., Winzeler, E.A. (2002). Excess Polymorphisms in Genes for Membrane Proteins in Plasmodium Falciparum. Science 298, 216-218 [Abs.]-[PDF]

In press/ Submitted