next up previous contents index
Next: Index Up: MODELLER A Program for Previous: TOP to Python correspondence   Contents   Index

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.

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 2007-08-03