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
General literature references
Next

[ afa94 | abo87 | all93 | ber77 | con83 | cri88 | eis86 | flo98 | fri96 | gon92 | hah93 | hal95 | hal99 | hei92 | hig92 | hut94 | kab83 | kly96 | kyt82 | mcl79 | mom75 | nee70 | nem83 | nem92 | pea88 | sai87 | shr73 | tho94 | thg94 | vea91 | wei86 | wei88 | wes92 | wil84 | zha92 ]

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  • Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., and Weng, J. (1987). Protein Data Bank. In: Crystallographic databases - Information content, software systems, scientific application eds. F. H. Allen, G. Bergerhoff, and R. Sievers, Data Commission of the International Union of Crystallography, Bonn/Cambridge/Chester, 107-132.
  • Allen, F.H., and Kennard O. (1993) 3D search and research using the Cambridge Structural Database. Chemical Design Automation News 8, pp. 1, 31-37.
  • Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi T., and Tasumi, M. (1994). The Protein Data Bank: A computer-based archival file for macromolecular structures recognition of distantly related proteins through energy calculations. J. Mol. Biol 112, 535-542.
  • Connolly, M.L. (1983). Analytical molecular surface calculation. J. Appl. Cryst. 16, 548-558.
  • Crippen, G.M. and Havel, T.F. (1988). Distance geometry and molecular conformation. Research Study Press, Ltd. (Wiley), New York.
  • Eisenberg, D. and McLachlan, A.D. (1986). Solvation energy in protein folding and binding. Nature 316, 199-203.
  • Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., Miller, W., (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 8, 967-974.
  • Frishman, D. and Argos, P. Incorporation of non-local interactions in protein secondary structure prediction form the amino acid sequence. Protein Eng. 9, 133-142.
  • Gonnet, G.H., Cohen, M.A., and Benner, S.A. (1992) Exhaustive matching of the entire protein sequence database. Science 256, 1433-1445.
  • Hahn, T. (ed.) (1993) International Tables for Crystallography, Vol. A, D. Reidel, Dordrecht.
  • Halgren, T.A. (1995) Merck Molecular Force Field. I.-V. J. Comp. Chem. 17, 490-641.
  • Halgren, T.A. (1999) MMFF VI. MMFF94s option for energy minimization studies. J. Comp. Chem. 20, 720-729.
  • Henikoff, S. and Henikoff, J.G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.
  • Higgins, D.G., Bleasby, A.J., and Fuchs, R. (1992). CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8, 189-191.
  • Hutchinson, E.G., and Thornton, J.M. (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci. 3, 2207-2215.
  • Kabsch, W. and Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
  • Kleywegt, G.J., and Jones, T.A. (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400.
  • Kyte, J. and Doolittle, R.F. (1982). J. Mol. Biol. 157 105-132.
  • McLachlan, A.D. (1979). Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol. 128, 49-79.
  • Momany, F.A., McGuire, R.F., Burgess, A.W., and Scheraga, H.A. (1975). Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79, 2361-2381.
  • Needleman, S.B. and Wunsch, C.D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
  • Nemethy, G., Pottle, M.S., and Scheraga, H.A. (1983). Energy parameters in polypeptides. 9. Updating of geometric parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87, 1883-1887.
  • Nemethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H.A. (1992). Energy Parameters in Polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96, 6472-6484.
  • Pearson, W.R., and Lipman, D.J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
  • Saitou, N. and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  • Shrake, A. and Rupley, J.A. (1973). Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79, 351-371.
  • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). Improved sensitivity of profile searches through the use of sequence weights and gap excision. CABIOS 10, 19-30.
  • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
  • Veal, J.M. and Wilson W.D. (1991). Modeling of nucleic acid complexes with cationic ligands: A specialized molecular mechanics force field and its application. J. Biomol. Struct. Dyn. 8, 1119-1145.
  • Weiner, S.J., Kollman, P.A., Nguyen, D.T., and Case, D.A. (1986). An all atom force field for simulation of proteins and nucleic acids. J. Comput. Chem. 7, 230-252.
  • Weininger, D. (1988) SMILES 1. Introduction and Encoding Rules J. Chem. Inf. Comput. Sci., 28, 31.
  • Wesson, L. and Eisenberg, D. (1992). Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1, 227-235.
  • Wilbur, W.J. and Lipman, D.J. (1984). The context dependent comparison of biological sequences. SIAM J. Appl. Math. 44, 557-567.
  • Zhang, X, Mesirov, J.P., and Waltz, D.L. Hybrid system for protein secondary structure prediction. J. Mol. Biol. 225, 1049-1063.


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