ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2020, Molsoft LLC Jun 5 2024
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[ abm88 | abm89 | aba92 | bor93 | bor94 | eis93 | maa89 | tab94 | doc94 | toa96 | abb97 | cad97 | baa99 | fta02 ]
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Totrov, M.M., and Abagyan, R.A. (1996).
The contour-buildup algorithm to calculate the analytical molecular surface.
J. Struct. Biol. 115, 1-6.
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Abagyan, R.A., and Batalov, S. (1997)
Do aligned sequences share the same fold?
J. Mol. Biol., 273, 1, 355-368.
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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.
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Batalov, S. and Abagyan, R.A., (1999)
Universal gap penalty for accurate global-local alignment of biological sequences
J. Mol. Biol., Molsoft report.
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Fernandez-Recio, J., Totrov, M., and Abagyan, R. (2002)
Soft Protein-Protein Docking in Internal Coordinates.
Protein Science, 11.
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