Abstract
The Protein Structure Initiative (PSI), funded by the US National Institutes of Health (NIH), provides a framework for the development and systematic evaluation of methods to solve protein structures. Although the PSI and other structural genomics efforts around the world have led to the solution of many new protein structures as well as the development of new methods, methodological bottlenecks still exist and are being addressed in this 'production phase' of PSI.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
BMC Bioinformatics Open Access 23 October 2015
-
Utilisation of adsorption and desorption for simultaneously improving protein crystallisation success rate and crystal quality
Scientific Reports Open Access 04 December 2014
-
Designing and benchmarking the MULTICOM protein structure prediction system
BMC Structural Biology Open Access 27 February 2013
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Levitt, M. Proc. Natl. Acad. Sci. USA 104, 3183–3188 (2007).
Chen, L., Oughtred, R., Berman, H.M. & Westbrook, J. Bioinformatics 20, 2860–2862 (2004).
Yooseph, S. et al. PLoS Biol. 5, e16 (2007).
Gill, S.R. et al. Science 312, 1355–1359 (2006).
Chandonia, J.M. & Brenner, S. Conf. Proc. IEEE Eng. Med. Biol. Soc. 1, 751–755 (2005).
Liu, J. & Rost, B. Nucleic Acids Res. 32, 3522–3530 (2004).
Stols, L. et al. Protein Expr. Purif. 25, 8–15 (2002).
Klock, H.E., Koesema, E.J., Knuth, M.W. & Lesley, S.A. Proteins, published online 14 November 2007 (doi:10.1093/bioinformatics/bth300).
Thao, S. et al. J. Struct. Funct. Genomics 5, 267–276 (2004).
Acton, T.B. et al. Methods Enzymol. 394, 210–243 (2005).
Klock, H.E., White, A., Koesema, E. & Lesley, S.A. J. Struct. Funct. Genomics 6, 89–94 (2005).
Blommel, P.G., Martin, P.A., Wrobel, R.L., Steffan, E. & Fox, B.G. Protein Expr. Purif. 47, 562–570 (2006).
Yu, P. et al. Cell Cycle 3, 75–79 (2004).
Stewart, L. & Burgin, A.B. in Frontiers in Drug Design and Discovery, Vol. 1. (eds., R. Atta Ur, B.A. Springer & G.W. Caldwell) 297–341 (Bentham Science Publishers, Ltd., Oak Park, Illinois, 2005).
Cooper, D.R. et al. Acta Crystallogr. D Biol. Crystallogr. 63, 636–645 (2007).
Brenner, S.E. Nat. Struct. Biol. 7 Suppl, 967–969 (2000).
Smialowski, P. et al. Curr. Protein Pept. Sci. 8, 121–133 (2007).
Goh, C.S. et al. J. Mol. Biol. 336, 115–130 (2004).
Watson, J.D. et al. IUBMB Life 55, 249–255 (2003).
Pantazatos, D. et al. Proc. Natl. Acad. Sci. USA 101, 751–756 (2004).
Studier, F.W. Protein Expr. Purif. 41, 207–234 (2005).
Strong, M., Sawaya, M.R., Wang, S., Phillips, M., Cascio, D. & Eisenberg, D. Proc. Natl. Acad. Sci. USA 103, 8060–8065 (2006).
Bashiri, G., Squire, C.J., Baker, E.N. & Moreland, N.J. Protein Expr. Purif. 54, 38–44 (2007).
Blommel, P.G., Becker, K.J., Duvnjak, P. & Fox, B.G. Biotechnol. Prog. 23, 585–598 (2007).
Suzuki, M., Roy, R., Zheng, H., Woychik, N. & Inouye, M. J. Biol. Chem. 281, 37559–37565 (2006).
Malkowski, M.G. et al. Proc. Natl. Acad. Sci. USA 104, 6678–6683 (2007).
Yokoyama, S. Curr. Opin. Chem. Biol. 7, 39–43 (2003).
Vinarov, D.A. & Markley, J.L. Expert Rev. Proteomics 2, 49–55 (2005).
White, M.A., Clark, K.M., Grayhack, E.J. & Dumont, M.E. J. Mol. Biol. 365, 621–636 (2007).
Roosild, T.P., Greenwald, J., Vega, M., Castronovo, S. & Choe, S. Science 307, 1317–1321 (2005).
Brown, E.N. & Ramaswamy, S. Acta Crystallogr. D Biol. Crystallogr. 63, 941–950 (2007).
Chayen, N.E. Methods Mol. Biol. 363, 175–190 (2007).
Kim, C.U., Hao, Q. & Gruner, S.M. Acta Crystallogr. D Biol. Crystallogr. 62, 687–694 (2006).
Slabinski, L., Jaroszewski, L, Rychlewski, L., Wilson, I.A. & Lesley, S.A. Bioinformatics 23, 3403–3405 (2007).
DiMaio, F., Shavlik, J. & Phillips, G.N. Bioinformatics 22, e81–e89 (2006).
Watson, J.D. et al. J. Mol. Biol. 367, 1511–1522 (2007).
Sidhu, S.S. & Kossiakof. A.A. Curr. Opin. Chem. Biol. 11, 347–354 (2007).
Mercier, K.A. et al. J. Am. Chem. Soc. 128, 15292–15299 (2006).
Aramini, J.M., Rossi, P., Anklin, C., Xiao, R. & Montelione, G. Nat. Methods 4, 491–493 (2007).
Eghbalnia, H.R. Bahrami, A., Tonelli, M., Hallenga, K. & Markley, J.L. J. Am. Chem. Soc. 127, 12528–12536 (2005).
Etezady-Esfarjani, T. Herrmann, T., Horst, R. & Wuthrich, K. J. Biomol. NMR 34, 3–11 (2006).
Acknowledgements
The Protein Structure Initiative is funded by NIH Institute of General Medical Sciences. We acknowledge all PSI workers, for their work created the materials and new knowledge that are the true value of the PSI.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
L.S. is the president of deCODE biostructures, Inc. deCODE biostructures, Inc. is a subsidiary of a publicly traded company, deCODE genetics, Inc.
Rights and permissions
About this article
Cite this article
Fox, B., Goulding, C., Malkowski, M. et al. Structural genomics: from genes to structures with valuable materials and many questions in between. Nat Methods 5, 129–132 (2008). https://doi.org/10.1038/nmeth0208-129
Issue Date:
DOI: https://doi.org/10.1038/nmeth0208-129
This article is cited by
-
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
BMC Bioinformatics (2015)
-
Utilisation of adsorption and desorption for simultaneously improving protein crystallisation success rate and crystal quality
Scientific Reports (2014)
-
Designing and benchmarking the MULTICOM protein structure prediction system
BMC Structural Biology (2013)
-
New LIC vectors for production of proteins from genes containing rare codons
Journal of Structural and Functional Genomics (2013)
-
The MULTICOM toolbox for protein structure prediction
BMC Bioinformatics (2012)