References for Results/Methods

References for the Results and Methods sections - Supplemental Materials in the publication

1. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E.L. Journal of molecular biology 305, 567-80 (2001).
2. Fagerberg, L., Jonasson, K., von Heijne, G., Uhlen, M. & Berglund, L. Proteomics 10, 1141-9 (2010).
3. Nugent, T. & Jones, D.T. PLoS computational biology 6, e1000714 (2010).
4. Kall, L., Krogh, A. & Sonnhammer, E.L. Journal of molecular biology 338, 1027-
36 (2004).
5. Kall, L., Krogh, A. & Sonnhammer, E.L. Bioinformatics 21 Suppl 1, i251-7 (2005).
6. Bernsel, A. et al. Proceedings of the National Academy of Sciences of the United States of America 105, 7177-81 (2008).
7. Viklund, H., Bernsel, A., Skwark, M. & Elofsson, A. Bioinformatics 24, 2928-9 (2008).
8. Zhou, H. & Zhou, Y. Protein science : a publication of the Protein Society 12, 1547-55 (2003).
9. Larsson, T.P., Murray, C.G., Hill, T., Fredriksson, R. & Schioth, H.B. FEBS Lett 579, 690-8 (2005).
10. Edgar, R.C. Bioinformatics 26, 2460-1 (2010).
11. Eswar, N. & Sali, A. in From Molecules to Medicine, Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism (eds. Sussman, J.L. & Spadon, P.) 139-151 (Springer-Verlag, Dordrecht, The Netherlands, 2009).
12. Pieper, U. et al. Nucleic Acids Research 39, D465-74 (2011).
13. Sanchez, R. & Sali, A. Proc Natl Acad Sci U S A 95, 13597-13602 (1998).
14. Altschul, S.F. et al. Nucleic acids research 25, 3389-402 (1997).
15. Sali, A. & Blundell, T.L. J Mol Biol 234, 779-815 (1993).
16. Smith, T.F. & Waterman, M.S. Journal of molecular biology 147, 195-7 (1981).
17. Eswar, N. et al. Current Protocols in Bioinformatics Chapter 5, Unit 5.6 (2006).
18. Marti-Renom, M.A., Madhusudhan, M.S. & Sali, A. Protein Sci 13, 1071-1087 (2004).
19. Dutta, S., Zardecki, C., Goodsell, D.S. & Berman, H.M. Journal of applied crystallography 43, 1224-1229 (2010).
20. Shen, M.Y. & Sali, A. Protein Sci 15, 2507-2524 (2006).
21. Melo, F., Sanchez, R. & Sali, A. Protein Sci 11, 430-448 (2002).
22. Eramian, D. et al. Protein Sci 15, 1653-1666 (2006).
23. Sanchez, R. & Sali, A. Methods Mol Biol 143, 97-129 (2000).
24. Johnson, M. et al. Nucleic acids research 36, W5-9 (2008).
25. Chen, L., Oughtred, R., Berman, H.M. & Westbrook, J. Bioinformatics 20, 2860-2 (2004).
26. Edgar, R.C. BMC bioinformatics 5, 113 (2004).
27. Vitkup, D., Melamud, E., Moult, J. & Sander, C. Nat Struct Biol 8, 559-66 (2001).
28. Nucleic acids research 40, D71-5 (2012).