-
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.
