International Journal of Quantum Chemistry

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Display, manipulation, and simulation of macromolecules

Shlomo Nir

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263

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Ramon Gardun̄o,

Ramon Gardun̄o

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263

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Robert Rein,

Corresponding Author

Robert Rein

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263Search for more papers by this author

Yves Coeckelenbergh,

Yves Coeckelenbergh

NASA-Ames Research Center, Moffett Field, California, 94035

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Robert D. Macelroy,

Robert D. Macelroy

NASA-Ames Research Center, Moffett Field, California, 94035

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John T. Egan,

John T. Egan

State University College at Buffalo, Buffalo, New York, 14263

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Shlomo Nir,

Shlomo Nir

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263

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Ramon Gardun̄o,

Ramon Gardun̄o

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263

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Robert Rein,

Corresponding Author

Robert Rein

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263

Roswell Park Memorial Institute, Buffalo, New York 14263, and Department of Biophysics, State University of New York at Buffalo, Buffalo, New York, 14263Search for more papers by this author

Yves Coeckelenbergh,

Yves Coeckelenbergh

NASA-Ames Research Center, Moffett Field, California, 94035

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Robert D. Macelroy,

Robert D. Macelroy

NASA-Ames Research Center, Moffett Field, California, 94035

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John T. Egan,

John T. Egan

State University College at Buffalo, Buffalo, New York, 14263

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First published: 9/12 January 1977

https://doi.org/10.1002/qua.560120714

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Abstract

A set of building and displaying programs has been written and applied to serve as tools in the study of the interaction of proteins with DNA and RNA. This study, which has involved the use of a variety of computers, is a collaborative project between the group at RPMI, Buffalo, New York, and NASA-Ames, California. The RPMI system, which is currently running on the Univac 70 computer, is easily adaptable to any computer, with or without sophisticated graphics hardware. Hence we emphasize the availability of an easy to handle and inexpensive means for building, displaying, and manipulating molecules. The RPMI system also includes an automated, nonin–teractive program for fast construction of specified molecular structures. The NASA system is running on an Evans and Sutherland display system which has sophisticated hardware and which is capable of continuously rotating the molecule with constant adjustment of perspective and intensity.

Bibliography

1 C. K. Johnson, OR TEP: A Fortran Thermal-Ellipsoid Plot Program for Crystal Structure Illustrations. ORNL–3794, 1965. Reprinted with minor revisions (1970).
Google Scholar
2 C. Levinthal, Sci. Am. 214, 42 (1966).
10.1038/scientificamerican0666-42
CAS PubMed Web of Science® Google Scholar
3 L. Katz and C. Levinthal, Ann. Rev. Biophys. Bioeng., 465 (1972).
Google Scholar
4 D. M. Collins, F. A. Cotton, E. E. Hazen, Jr., E. F. Meyer, and C. N. Morimoto, Science 190, 1047 (1975).
10.1126/science.1188383
CAS PubMed Web of Science® Google Scholar
5 C. D. Barry, H. E. Bosshard, R. A. Ellis, and G. R. Marshall, Federation Proc. 33, 2368 (1975).
PubMed Web of Science® Google Scholar
6 S. D. Stellman, Macromol. 7, 296 (1974).
10.1021/ma60039a008
CAS PubMed Web of Science® Google Scholar
7 N. Gδ and H. A. Scheraga, Macromol. 3, 178 (1970).
10.1021/ma60014a012
CAS Google Scholar
8 S. C. Jain and H. Sobell, J. Mol. Biol. 68, 1 (1972).
10.1016/0022-2836(72)90258-6
CAS PubMed Web of Science® Google Scholar
9 P. DeSantis, E. Forni, and R. Rizzo, Biopolym. 13, 313 (1974).
10.1002/bip.1974.360130207
CAS PubMed Web of Science® Google Scholar
10 C. C. Tsai, S. S. Jain, and H. M. Sobell, Phil. Trans. Roy. Soc. (London) 272-B, 137 (1975).
10.1098/rstb.1975.0076
Web of Science® Google Scholar
11 C. W. Carter, Jr. and J. Kraut, Proc. Nat. Acad. Sci. 71, 283 (1974).
10.1073/pnas.71.2.283
CAS PubMed Web of Science® Google Scholar
12 T. Maniatis and M. Ptashne, Nature 246, 133 (1973).
10.1038/246133a0
CAS PubMed Web of Science® Google Scholar
13 G. V. Gursky, V. G. Tumanyan, A. S. Zasedatelev, A. L. Zhuze, S. L. Grokhovsky, and B. P. Gottikh, Mol. Biol. Rep. 2, 427 (1976).
10.1007/BF00366265
CAS PubMed Web of Science® Google Scholar
14 H. Murakami, H. Mori, and S. Taira, J. Theor. Biol. 59, 1 (1976).
10.1016/S0022-5193(76)80021-5
CAS PubMed Web of Science® Google Scholar
15 K. D. Gibson and H. A. Scheraga, Proc. Nat. Acad. Sci. (U.S.A.) 58, 420 (1967).
10.1073/pnas.58.2.420
CAS PubMed Web of Science® Google Scholar
16 H. A. Scheraga, Adv. Phys. Org. Chem. 6, 103 (1968).
10.1016/S0065-3160(08)60255-5
CAS Google Scholar
17 G. Alagona, A. Pullman, E. Scrocco, and J. Tomasi, Int. F. Peptide Protein Res. 5, 25 (1973).
Google Scholar
18 D. L. Beveridge, M. M. Kelly, and R. J. Radna, J. Amer. Chem. Soc. 96, 3769 (1974).
10.1021/ja00819a010
CAS PubMed Web of Science® Google Scholar
19 A. J. Hopfinger, Macromol. 4, 731 (1971).
10.1021/ma60024a012
CAS Web of Science® Google Scholar
20 B. Pullman and B. Maigret in Conformation of Biological Molecules and Polymers, E. D. Bergmann and B. Pullman, Eds. (Israel Acad, of Sciences and Humanities, Jerusalem, Israel, 1973), p. 13.
Google Scholar
21 R. Rein, V. Renugopalakrishnan, S. Nir, and T. J. Swissler, Int. J. Quantum Chem. QBS 2, 99 (1975).
CAS Google Scholar
22 F. A. Momany, R. F. McGuire, and H. A. Scheraga, J. Phys. Chem. 79, 2361 (1975).
10.1021/j100589a006
CAS Web of Science® Google Scholar
23 V. Renugopalakrishnan, S. Nir, and R. Rein in Environmental Effects on Molecular Structure and Properties, B. Pullman, Ed., Israel National Academy of Sciences (Reidel Publ., Dordrecht, Netherlands, 1976), pp. 109–133.
Google Scholar
24 M. Levitt, J. Mol. Biol. 104, 59 (1976).
10.1016/0022-2836(76)90004-8
CAS PubMed Web of Science® Google Scholar
25 S. Nir, R. Garduno, R. Rein, and R. D. MacElroy, Polymer (in press).
Google Scholar
26 IUPAC-IUB Commission on Biochemical Nomenclature, Biochem. 9, 3471 (1970).
10.1021/bi00820a001
PubMed Web of Science® Google Scholar