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Suggested Citation:"REFERENCES." National Research Council. 1995. Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology. Washington, DC: The National Academies Press. doi: 10.17226/2121.
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Suggested Citation:"REFERENCES." National Research Council. 1995. Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology. Washington, DC: The National Academies Press. doi: 10.17226/2121.
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Page 268
Suggested Citation:"REFERENCES." National Research Council. 1995. Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology. Washington, DC: The National Academies Press. doi: 10.17226/2121.
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Page 269
Suggested Citation:"REFERENCES." National Research Council. 1995. Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology. Washington, DC: The National Academies Press. doi: 10.17226/2121.
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Page 270
Suggested Citation:"REFERENCES." National Research Council. 1995. Calculating the Secrets of Life: Contributions of the Mathematical Sciences to Molecular Biology. Washington, DC: The National Academies Press. doi: 10.17226/2121.
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Page 271

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FOLDING THE SHEETS: USING COMPUTATIONAL METHODS TO PREDICT THE STRUCTURE OF PROTEINS 267 REFERENCES Anfinsen, C.B., E. Haber, M. Sela, and F.H. White, 1961, "The kinetics of the formation of native ribonuclease during oxidation of the reduced polypeptide domain," Proceedings of the National Academy of Sciences USA 47, 1309-1314. Barton, G.J., and M.J.E. Sternberg, 1987, "Evaluation and improvements in the automatic alignment of protein sequences," Protein Engineering 1, 89-94. Blundell, T.L., and L.N. Johnson, 1976, Protein Crystallography, New York: Academic Press. Bowie, J.U., R. Luthy, and D. Eisenberg, 1991, "A method to identify protein sequences that fold into a known 3-dimensional structure," Science 253, 164-170. Bruccoleri, R.E., and M. Karplus, 1987, "Prediction of the folding of short polypeptide segments by uniform conformational sampling," Biopolymers 26, 137-168. Chothia, C., 1974, "Hydrophobic bonding and accessible surface area in proteins," Nature 248, 338-339. Chothia, C., and A.M. Lesk, 1986, "The relation between divergence of sequence and structure in proteins," EMBOJ. 5, 823-826. Chothia, C., A.M. Lesk, A. Tramontano, M. Levitt, S.J. Smith-Gill, G. Air, S. Sheriff, E.A. Padlan, D. Davies, and W.R. Tulip, 1989, "Conformations of immunoglobulin hypervariable regions," Nature 343, 877-883. Chothia, C., M. Levitt, and D. Richardson, 1977, "Structure of proteins: Packing of a-helices and pleated sheets," Proceedings of the National Academy of Sciences USA 74, 4130-4134. Chou, P.Y., and G.D. Fasman, 1974, "Conformational parameters for amino acids on helical, b-sheet, and random coil regions calculated from proteins," Biochemistry 13, 211-245. Cohen, F.E., M.J.E. Sternberg, and W.R. Taylor, 1980, "Analysis and prediction of protein b-sheet structures by a combinatorial approach," Nature 285, 378-382. Cohen, F.E., M.J.E. Sternmerb, and W.R. Taylor, 1982, "The analysis and prediction of tertiary structure of globular proteins involving the packing of a-helices against a b-sheet: A combinatorial approach," Journal of Molecular Biology 156, 821-862. Cohen, F.E., R.A. Abarbanel, I.D. Kuntz, and R.J. Fletterick, 1983, "Secondary structure assignment for a/b proteins by a combinatorial approach," Biochemistry 22, 4894-4904. Cohen, F.E., R.A. Abarbanel, I.D. Kuntz, and R.J. Fletterick, 1986, "Turn prediction in proteins using a pattern-matching approach," Biochemistry 25, 266-275. Cohen, F.E., and I.D. Kuntz, 1989, "Tertiary structure predictions," pp. 647-706 in Prediction of Protein Structure and the Principles of Protein Conformation, G.D. Fasman (ed.), New York: Plenum. Cohen, F.E., T.J. Richmond, and F.M. Richards, 1979, "Protein folding: Evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example," Journal of Molecular Biology 132, 275-288. Crick, F.H.C., 1953, "The packing of a-helices: Simple coiled coils," Acta Crystallogr. 6, 689-697.

FOLDING THE SHEETS: USING COMPUTATIONAL METHODS TO PREDICT THE STRUCTURE OF PROTEINS 268 Crippen, G.M., and T.F. Havel, 1988, Distance Geometry and Molecular Conformation, New York: John Wiley & Sons. Dayhoff, M.O., L.T. Hunt, P.J. McLaughlin, and D.D. Jones, 1972, "Gene duplications in evolution: The globins," pp. 17-30 in Atlas of Protein Sequence and Structure, Vol. 5, M.O. Dayhoff (ed.), Silver Spring, Md.: National Biomedical Research Foundation. Dorit, R.L., L. Schoenbach, and W. Gilbert, 1990, "How big is the universe of exons?" Science 250, 1377-1382. Finkelstein, A.V., and B.A. Reva, 1991, "A search for the most stable folds of protein chains," Nature 351, 497-499. Fischer, G., and F.X. Schmid, 1991, "The mechanism of protein folding: Implications of in vitro refolding mode for de novo protein folding and translocation in the cell," Biochemistry 29, 2205-2212. Frauenfelder, H., H. Hartmann, M. Karplus, I.D. Kuntz, Jr., J. Kuriyan, F. Darak, G.A. Petsko, D. Ringe, R.F. Tilton, Jr., and M.L. Connolly, 1987, "Thermal expansion of a protein," Biochemistry 26, 254-261. Freedman, R.B., 1989, "Protein disulfide isomerase: Multiple roles in the modification of nascent secretory proteins," Cell 57, 1069-1072. Garier, J., D.J. Osguthorpe, and B. Robson, 1978, "Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins," Journal of Molecular Biology 120, 97-120. Gilson, M.K., and B.H. Honig, 1986, "The dielectric constant of a folded protein," Biopolymers 25, 2097-2119. Gonnet, G.H., M.A. Cohen, and S.A. Benner, 1992, "Exhaustive matching of the entire protein sequence database," Science 256, 1443-1445. Greer, J., 1990, "Comparative modeling methods: Application to the family of the mammalian serine proteases," Proteins Struct. Funct. Genet. 7, 317-334. Gregoret, L.M., and F.E. Cohen, 1990, "Novel method for the rapid evaluation of packing in protein structures," Journal of Molecular Biology 211, 959-974. Hagler, A.T., and B. Honig, 1978, "On the formation of protein tertiary structure on a computer," Proceedings of the National Academy of Sciences USA 75, 554-558. Holley, L.H., and M. Karplus, 1989, "Protein secondary structure prediction with a neural network," Proceedings of the National Academy of Sciences USA 86, 152-156. Howard, A.E., and P.A. Kollman, 1988, "An analysis of current methodologies for conformational searching of complex molecules," J. Med. Chem. 31, 1675-1679. Jones, T.A., and S. Thirup, 1986, "Using known substructures in protein model building and crystallography," EMBOJ. 5, 819-822. Kabsch, W., and C. Sander, 1984, "On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations," Proceedings of the National Academy of Sciences USA 81, 1075-1078. Karlin, S., and S.F. Altschul, 1990, "Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes," Proceedings of the National Academy of Sciences USA 87, 2264-2268. Kauzmann, W., 1959, "Some factors in the interpretation of protein denaturation," Adv. Protein Chem. 14, 1-63. Kendrew, J.C., 1963, "Myoglobin and the structure of proteins," Science 139, 1259-1266.

FOLDING THE SHEETS: USING COMPUTATIONAL METHODS TO PREDICT THE STRUCTURE OF PROTEINS 269 King, R.D., and M.J.E. Sternberg, 1990, "Machine learning approach for the prediction of protein secondary structure," Journal of Molecular Biology 216, 441-457. Kneller, D.G., F.E. Cohen, and R. Langridge, 1990, "Improvements in protein secondary structure prediction by an enhanced neural network," Journal of Molecular Biology 214, 171-182. Konigsberg, W.H., and H.M. Steinman, 1977, "Strategy and methods of sequence analysis," pp. 1-178 in The Proteins, Vol. 3, 3rd ed., H. Neurath and R.L. Hill (eds.), New York: Academic Press. Kumamoto, C.A., 1991, "Molecular chaperones and protein translocation across the Escherichia coli inner membrane," Molecular Microbiology 5, 19-22. Kuwajima, K., 1989, "The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure," Proteins Struct. Funct. Genet. 6, 87-103. Lee, B., and F.M. Richards, 1971, "The interpretation of protein structures: Estimation of solvent accessibility," Journal of Molecular Biology 55, 379-400. Lesser, G.J., and G.D. Rose, 1990, "Hydrophobicity of amino acid subgroups in proteins," Proteins Struct. Funct. Genet. 8, 6-13. Levitt, M., 1976, "A simplified representation of protein structures and implications for protein folding," Journal of Molecular Biology 104, 59-107. Levitt, M., and C. Chothia, 1976, "Structural patterns in globular proteins," Nature 261, 552-558. Lifson, S., and A. Warshel, 1969, "Consistent force field for calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules," J. Chem. Phys. 49, 5116-5129. Lim, V.I., 1974, "Structural principles of the globular organization of protein chains: A stereochemical theory of globular protein secondary structure," Journal of Molecular Biology 88, 857-894. Linderstrom-Lang, K.V., and J.A. Schellman, 1959, "Protein structure and enzyme activity," pp. 443-510 in The Enzymes, Vol. 1, P.D. Boyer (ed.), New York: Academic Press. Maxam, A., and W. Gilbert, 1980, "Nucleic acids Part I," pp. 499-560 in Methods in Enzymology, Vol. 65, L. Grossman and K. Moldave (eds.), New York: Academic Press. Murzin, A.G., and A.V. Finkelstein, 1988, "General architecture of the alpha-helical globule," Journal of Molecular Biology 204, 749-769. Novotny, J., A.A. Rashin, and R.E. Bruccoleri, 1988, "Criteria that discriminate between native proteins and incorrectly folded models," Proteins Struct. Funct. Genet. 4, 19-30. Overington, J., M.S. Johnson, A. Sali, and T. L. Blundell, 1990, "Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction," Proceedings of the Royal Society of London, Series B: Biological Sciences 241, 132-145. Padmanabhan, S., S. Marqusee, T. Ridgeway, T.M. Laue, and R.L. Baldwin, 1990, "Relative helix-forming tendencies of nonpolar amino acids," Nature 344, 268-270. Pauling, L., 1967, The Chemical Bond: A Brief Introduction to Modern Structural Chemistry, Ithaca, N.Y.: Cornell University Press.

FOLDING THE SHEETS: USING COMPUTATIONAL METHODS TO PREDICT THE STRUCTURE OF PROTEINS 270 Pauling, L., R.B. Corey, and H.R. Branson, 1951, "The structure of proteins: Two hydrogen bonded helical configurations of the polypeptide chain," Proceedings of the National Academy of Sciences USA 37, 205-211. Pearl, L.H., and W.R. Taylor, 1987, "A structural model for the retroviral proteases," Nature 329, 351-354. Ponder, J.W., and F.M. Richards, 1987, "Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes," Journal of Molecular Biology 193, 775-791. Presnell, S.R., B.I. Cohen, and F.E. Cohen, 1992, "A segment based approach to protein structure prediction," Biochemistry 31, 983-993. Presnell, S.R., and F.E. Cohen, 1989, "Topological distribution of four-alpha-helix bundles," Proceedings of the National Academy of Sciences USA 86, 6592-6596. Ptitsyn, O.B., and A.A. Rashin, 1975, "A model of myoglobin self-organization," Biophys. Chem. 3, 1-20. Qian, N., and T.J. Sejnowski, 1988, "Predicting the secondary structure of globular proteins using neural network models," Journal of Molecular Biology 202, 865-884. Richards, F.M., 1977, "Areas, volumes, packing, and protein structure," Annu. Rev. Biophys. Bioeng. 6, 151-176. Richmond, T.J., 1984, "Solvent accessible surface area and excluded volume in proteins," Journal of Molecular Biology 176, 63-89. Richmond, T.J., and F.M. Richards, 1978, "Packing of a-helices: Geometrical constraints and contact areas," Journal of Molecular Biology 119, 537-555. Rumelhart, D.E., G.E. Hinton, and R.J. Williams, 1986, Parallel Distributed Processing. Explorations in the Microstructure of Cognition, Vol. 1, Cambridge, Mass.: MIT Press, pp. 318-362. Sippl, M.J., 1990, "Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins," Journal of Molecular Biology 213, 859-883. Smith, R.F., and T.F. Smith, 1990, "Automation generation of primary sequence patterns from sets of related protein sequences," Proceedings of the National Academy of Sciences USA 87, 118-122. Smith, T.F., and M.S. Waterman, 1981, "Comparison of biosequences," Adv. Appl. Math. 2, 482. Sondek, J., and D. Shortle, 1990, "Accommodation of single amino acid insertions by the native state staphylococcal nuclease," Proteins Struct. Funct. Genet. 7, 299-305. Troyer, J.M., and F.E. Cohen, 1991, "Simplified models for understanding and predicting protein structure," pp. 57-80 in Reviews in Computational Chemistry, K.B. Lipkowitz and D.B. Boyd (eds.), New York: VCH Publishers, Inc. Wendoloski, J.J., and F.R. Salemme, 1992, "PROBIT-A statistical approach to modeling proteins from partial coordinate data using substructure libraries," J Molec. Graphics 10, 124-126. Wierenga, R.K., and W.G. Hol, 1993, "Predicted nucleotide binding properties of p21 protein and its cancer associated variant," Nature 302, 842-844. Wilson, C., and S. Doniach, 1989, "A computer model to dynamically simulate protein folding: Studies with Crambin," Proteins Struct. Funct. Genet. 6, 193-209.

FOLDING THE SHEETS: USING COMPUTATIONAL METHODS TO PREDICT THE STRUCTURE OF PROTEINS 271 Wilson, C., L.M. Gregoret, and D.A. Agard, 1993, "Modeling side-chain conformation for homologous proteins using an energy-based rotamer search," Journal of Molecular Biology 229, 996-1006. Wuthrich, K., 1986, NMR of Proteins and Nucleic Acids, New York: John Wiley & Sons.

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As researchers have pursued biology's secrets to the molecular level, mathematical and computer sciences have played an increasingly important role—in genome mapping, population genetics, and even the controversial search for "Eve," hypothetical mother of the human race.

In this first-ever survey of the partnership between the two fields, leading experts look at how mathematical research and methods have made possible important discoveries in biology.

The volume explores how differential geometry, topology, and differential mechanics have allowed researchers to "wind" and "unwind" DNA's double helix to understand the phenomenon of supercoiling. It explains how mathematical tools are revealing the workings of enzymes and proteins. And it describes how mathematicians are detecting echoes from the origin of life by applying stochastic and statistical theory to the study of DNA sequences.

This informative and motivational book will be of interest to researchers, research administrators, and educators and students in mathematics, computer sciences, and biology.

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