ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 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 algorithms
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[ abm88 | abm89 | aba92 | bor93 | bor94 | eis93 | maa89 | tab94 | doc94 | toa96 | abb97 | cad97 | baa99 | fta02 ]

  • 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.
  • Batalov, S. and Abagyan, R.A., (1999) Universal gap penalty for accurate global-local alignment of biological sequences J. Mol. Biol., Molsoft report.
  • Fernandez-Recio, J., Totrov, M., and Abagyan, R. (2002) Soft Protein-Protein Docking in Internal Coordinates. Protein Science, 11.


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