## Bibliography

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.

Dong et al., 2013
  Dong, G. Q., Fan, H., Schneidman-Duhovny, D., Webb, B., & Sali, A. (2013).
  Bioinformatics, Epub ahead of print.
  (Also available online).

Felsenstein, 1985
  Felsenstein, J. (1985).
  Evolution, 39, 783-791.

Fiser et al., 2000
  Fiser, A., Do, R. K. G., & Šali, A. (2000).
  Protein Sci. 9, 1753-1773.
  (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 & Šali, 2003
  John, B. & Šali, 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., Martı-Renom, M. A., Sanchez, R., & Šali, A. (2006).
  Prot. Eng. Des. & Sel. 19, 129-133.
  (Also available online).

Madhusudhan et al., 2009
  Madhusudhan, M. S., Webb, B. M., Martı-Renom, M. A., Eswar, N., & Šali, A. (2009).
  Prot. Eng. Des. & Sel. 22 (9), 569-574.
  (Also available online).

Martı-Renom et al., 2004
  Martı-Renom, M. A., Madhusudhan, M. S., & Šali, 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., & Šali, 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.

Pearson, 1998
  Pearson, W. (1998).
  J. Mol. Biol. 276, 71-84.

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.

Šali & Blundell, 1990
  Šali, A. & Blundell, T. L. (1990).
  J. Mol. Biol. 212, 403-428.
  (Also available online).

Šali & Blundell, 1993
  Šali, A. & Blundell, T. L. (1993).
  J. Mol. Biol. 234, 779-815.
  (Also available online).

Šali & Overington, 1994
  Šali, 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).

Shen & Šali, 2006
  Shen, M.-Y. & Šali, A. (2006).
  Protein Sci. 15, 2507-2524.
  (Also available online).

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., & Šali, 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.