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.
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.
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.
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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