ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2020, Molsoft LLC Jun 5 2024
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[ car95 | bok95 | str96 | cha96 | tha97 | goc96 | mai97 | yuj97 | isa98 | mai98 | pat98 | sri98 | zho98 | jcp99 | zha99 | zho99 | sch99 | sti99 | tom00 | gat99 | lid00 | sch00 ]
Some applications of the ICM program are described in the following publications
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Cardozo, T., Totrov, M., and Abagyan, R. (1995)
Homology modeling by the ICM method.
Proteins 23, 403-414 .
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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.
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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.
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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.
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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.
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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.
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Maiorov, V.N. and Abagyan, R.A. (1997)
A new method for modeling large-scale rearrangements of protein domains.
Proteins 27, 410-424.
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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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Isakoff SJ, Cardozo T, Andreev J, Li Z, Ferguson KM, Abagyan R, Lemmon MA,Aronheim A, Skolnik EY (1998)
Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast.
EMBO J , 17, 5374-5387.
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Maiorov, V.N. and Abagyan, R.A. (1998)
Energy strain in three-dimensional protein structures
Folding and Design, 3 , 259-269.
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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.
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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, 581-591.
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Zhou, Y., and Abagyan, R.A. (1998)
How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains.
Folding and Design, 3, 513-522.
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Abagyan, R., and Totrov, M. (1999)
Ab Initio Folding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure
J. Comp. Phys., 151, 402-421.
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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(16), 10969-74.
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Zhou, Y., and Abagyan, R.A. (1999)
Efficient stochastic global optimization for protein structure prediction
Rigidity Theory and Application, (Thorpe, M., ed.), (in press), .
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Schapira, M., Totrov, M., and Abagyan, R. (1999)
Prediction of the binding energy for small molecules, peptides and proteins.
J. Mol. Recognition, 12, 177-190.
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Stigler, R.D., Hoffmann, B., Abagyan, R., Schneider-Mergener, J. (1999)
Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics.
Structure Fold Des , 7, 663-670 .
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Tomko RP, Johansson CB, Totrov M, Abagyan R, Frisen J, Philipson L (2000)
Expression of the adenovirus receptor and its interaction with the fiber knob
Exp Cell Res, 255, 47-55.
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Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D,Abagyan R, Schier AF, Talbot WS (1999)
A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences.
Genome Res., 9, 334-347.
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Li, D., Desai-Yajnik, V., Lo E., Schapira, M., Abagyan, R., Samuels, H.H. (1999)
NRIF3 is a novel coactivator mediating functional specificity
of nuclear hormone receptors.
Mol Cell Biol 19, 7191-7202.
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Schapira, M., Raaka, B.M., Samuels, H.H., Abagyan, R. (2000)
Rational discovery of novel nuclear hormone receptor antagonists.
Proc Natl Acad Sci U S A 97, 1008-1013.
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