References (1zkd)

References

• Baker, N.A., Sept, D., Joseph, S., Holst, M.J. & McCammon, J.A. (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci., 98, 10037-10041.

• DeLano, W.L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, Palo Alto, CA, USA.

• Fink, J.L., Aturaliya, R.N., Davis, M.J., Zhang, F., Hanson, K., Teasdale, M.S., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y. & Teasdale, R.D. (2006). LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res., 34(Database issue),D213-7.

• Gough, J., Karplus, K., Hughey, R. & Chothia, C. (2001). Assignment of homology to genome sequences using a library of Hidden Markov Models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.

• Hawkins, J., Davis, L. & Bodén, M. (2006). Predicting Nuclear Proteins. Manuscript Submitted to Bioinformatics.

• Krissinel, E. & Henrick, K. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst., D60, 2256-2268.

• Laskowski, R. A., Watson, J. D. & Thornton, J. M. (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93.

• Laskowski, R.A., Watson, J.D. & Thornton, J.M. (2005). Protein function prediction using local 3D templates. J. Mol. Biol., 351, 614-626.

• Madera, M., Vogel, C., Kummerfeld, S.K., Chothia, C. & Gough, J. (2004). The SUPERFAMILY database in 2004: additions and improvements. Nucl. Acids Res., 32, D235-D239.

• Schubert, H.L., Blumenthal, R.M. & Cheng, X. (2003). Many paths to methyltransfer: a chronicle of convergence. Trends in Biochemical Sciences, 28 (6),329-335.

• Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JL, Peres C, Harrison FH, Gibson J, Harwood CS (2004). Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol. 2004 Jan;22(1):55-61.

• Joseph Felsenstein. (1991-2004). SEQBOOT -- Bootstrap, Jackknife, or Permutation Resampling of Molecular Sequence, Restriction Site, Gene Frequency or Character Data. University of Washington - http://evolution.genetics.washington.edu/phylip/doc/seqboot.html.

• Joseph Felsenstein. (1993, 2000-2004). PROTDIST -- Program to compute distance matrix from protein sequences. University of Washington - http://evolution.genetics.washington.edu/phylip/doc/protdist.html.

• Joseph Felsenstein. (1986-2004). CONSENSE -- Consensus tree program. University of Washington - http://evolution.genetics.washington.edu/phylip/doc/consense.html.

• Ruslan I. Sadreyev, David Baker and Nick V. Grishin. (2003). Profile–profile comparisons by COMPASS predict intricate homologies between protein families. Protein Science (2003), 12:2262-2272.

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