ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Oct 18 2018

Contents
 
Introduction
Reference Guide
Command Line User's Guide
References
 References
 ICM refs
 ICM algorithms
 ICM applications
 Credits
Glossary
 
Index
PrevICM Language Reference
ICM applications
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Some applications of the ICM program are described in the following publications
  • 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.
  • 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.
  • Maiorov, V.N. and Abagyan, R.A. (1998) Energy strain in three-dimensional protein structures Folding and 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, 581-591.
  • 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.
  • 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.
  • 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.
  • Zhou, Y., and Abagyan, R.A. (1999) Efficient stochastic global optimization for protein structure prediction Rigidity Theory and Application, (Thorpe, M., ed.), (in press), .
  • 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.
  • 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 .
  • 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.
  • 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.
  • 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.
  • 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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