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     Contents 
     Index 
- Braun & Gõ, 1985
 - 
Braun, W. & Gõ, N. (1985).
J. Mol. Biol. 186, 611-626.
 - Brünger, 1992
 - 
Brünger, A. T. (1992).
X-PLOR Manual Version 3.1.
Yale University New Haven, Connecticut.
 - Felsenstein, 1985
 - 
Felsenstein, J. (1985).
Evolution,  39, 783-791.
 - Fiser et al., 2000
 - 
Fiser, A., Do, R. K. G., & Š
ali, A. (2000).
Protein Sci. 9, 1-21.
(Also available
  online).
 - Gallicchio & Levy, 2004
 - 
Gallicchio, E. & Levy, R. M. (2004).
J. Comp. Chem. 25, 479-499.
 - Goldstein, 1980
 - 
Goldstein, H. (1980).
Classical Mechanics, 2nd edition.
Reading, Massachusetts: Addison-Wesley Publishing Company.
 - Gotoh, 1982
 - 
Gotoh, O. (1982).
J. Mol. Biol. 162, 705-708.
 - Hubbard & Blundell, 1987
 - 
Hubbard, T. J. P. & Blundell, T. L. (1987).
Protein Eng. 1, 159-171.
 - IUPAC-IUB, 1970
 - 
IUPAC-IUB (1970).
Biochem. 9, 3471-3479.
 - John & Š
ali, 2003
 - 
John, B. & Š
ali, A. (2003).
Nucl. Acids Res. 31, 3982-3992.
(Also available
  online).
 - Kabsch & Sander, 1983
 - 
Kabsch, W. & Sander, C. (1983).
Biopolymers,  22, 2577-2637.
 - Karlin & Altschul, 1990
 - 
Karlin, S. & Altschul, S. F. (1990).
Proc. Natl. Acad. Sci. USA,  87, 2264-2268.
 - Kendrew et al., 1970
 - 
Kendrew, J. C., Klyne, W., Lifson, S., Miyazawa, T., Némethy, G.,
  Phillips, D. C., Ramachandran, G. N., & Scheraga, H. (1970).
J. Mol. Biol. 52, 1-17.
 - Loncharich et al., 1992
 - 
Loncharich, R. J., Brooks, B. R., & Pastor, R. W. (1992).
Biopolymers,  32, 523-535.
 - MacKerell et al., 1998
 - 
MacKerell, Jr., A. D., Bashford, D., Bellott, M., Dunbrack Jr., R. L.,
  Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S.,
  Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C.,
  Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, III, W. E., Roux,
  B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M.,
  Wiorkiewicz-Kuczera, J., Yin, D., & Karplus, M. (1998).
J. Phys. Chem. B,  102, 3586-3616.
 - Madhusudhan et al., 2006
 - 
Madhusudhan, M. S., Martí-Renom, M. A., Sanchez, R., & Š
ali, A.
  (2006).
Prot. Eng. Des. & Sel. 19, 129-133.
(Also available
  online).
 - Martí-Renom et al., 2004
 - 
Martí-Renom, M. A., Madhusudhan, M. S., & Š
ali, A. (2004).
Protein Sci. 13, 1071-1087.
(Also available
  online).
 - Melo & Feytmans, 1997
 - 
Melo, F. & Feytmans, E. (1997).
J. Mol. Biol. 267, 207-222.
 - Melo et al., 2002
 - 
Melo, F., Sánchez, R., & Š
ali, A. (2002).
Protein Sci. 11, 430-448.
(Also available
  online).
 - Metropolis et al., 1953
 - 
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., & Teller,
  E. (1953).
J. Chem. Phys. 21, 1087-1092.
 - Needleman & Wunsch, 1970
 - 
Needleman, S. B. & Wunsch, C. D. (1970).
J. Mol. Biol. 48, 443-453.
 - Nicholls et al., 1991
 - 
Nicholls, A., Sharp, K. A., & Honig, B. (1991).
Proteins,  11, 281-296.
 - Press et al., 1992
 - 
Press, W. H., Teukolsky, S. A., Vetterling, W. T., & Flannery, B. P. (1992).
Numerical Recipes, 2nd edition.
Cambridge: Cambridge University Press.
 - Rapaport, 1997
 - 
Rapaport, D. C. (1997).
The Art of Molecular Dynamics Simulation.
Cambridge, UK: Cambridge University Press.
 - Richards & Kundrot, 1988
 - 
Richards, F. M. & Kundrot, C. E. (1988).
Proteins,  3, 71-84.
 - Richmond & Richards, 1978
 - 
Richmond, T. J. & Richards, F. M. (1978).
J. Mol. Biol. 119, 537-555.
 - Š
ali & Blundell, 1990
 - 
Š
ali, A. & Blundell, T. L. (1990).
J. Mol. Biol. 212, 403-428.
(Also available
  online).
 - Š
ali & Blundell, 1993
 - 
Š
ali, A. & Blundell, T. L. (1993).
J. Mol. Biol. 234, 779-815.
(Also available
  online).
 - Š
ali & Overington, 1994
 - 
Š
ali, A. & Overington, J. (1994).
Protein Sci. 3, 1582-1596.
(Also available
  online).
 - Sankoff & Kruskal, 1983
 - 
Sankoff, D. & Kruskal, J. B. (1983).
Time warps, string edits, and macromolecules: The theory and
  practice of sequence comparison.
Reading, MA: Addison-Wesley Publishing Company.
 - Sellers, 1974
 - 
Sellers, P. H. (1974).
J. Comb. Theor. A16, 253-258.
 - Shanno & Phua, 1980
 - 
Shanno, D. F. & Phua, K. H. (1980).
ACM Trans. Math. Soft. 6, 618-622.
 - Shanno & Phua, 1982
 - 
Shanno, D. F. & Phua, K. H. (1982).
In: Collected algorithms from ACM. Trans. Math. Software
  volume 2(1).
 - Smith & Waterman, 1981
 - 
Smith, T. F. & Waterman, M. S. (1981).
J. Mol. Biol. 147, 195-197.
 - Subbiah et al., 1993
 - 
Subbiah, S., Laurents, D. V., & Levitt, M. (1993).
Curr. Biol. 3, 141-148.
 - Sutcliffe et al., 1987
 - 
Sutcliffe, M. J., Haneef, I., Carney, D., & Blundell, T. L. (1987).
Protein Eng. 1, 377-384.
 - Topf et al., 2005
 - 
Topf, M., Baker, M. L., John, B., Chiu, W., & Š
ali, A. (2005).
J. Struct. Biol. 149, 191-203.
(Also available
  online).
 - van Schaik et al., 1993
 - 
van Schaik, R. C., Berendsen, H. J., & Torda, A. E. (1993).
J. Mol. Biol. 234, 751-762.
 - Verlet, 1967
 - 
Verlet, J. (1967).
Phys. Rev. 159, 98-103.
 - Wu & Brooks, 2003
 - 
Wu, X. & Brooks, B. R. (2003).
Chem. Phys. Lett. 381, 512-518.
 - Wu & Wang, 1999
 - 
Wu, X. & Wang, S. (1999).
J. Chem. Phys. 110, 9401-9410.
 
Ben Webb
2007-01-19