Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 20 January 2006:
Vol. 311. no. 5759, pp. 347 - 351
DOI: 10.1126/science.1121018

Review

The Impact of Structural Genomics: Expectations and Outcomes

John-Marc Chandonia and Steven E. Brenner*

Structural genomics (SG) projects aim to expand our structural knowledge of biological macromolecules while lowering the average costs of structure determination. We quantitatively analyzed the novelty, cost, and impact of structures solved by SG centers, and we contrast these results with traditional structural biology. The first structure identified in a protein family enables inference of the fold and of ancient relationships to other proteins; in the year ending 31 January 2005, about half of such structures were solved at a SG center rather than in a traditional laboratory. Furthermore, the cost of solving a structure at the most efficient SG center in the United States has dropped to one-quarter of the estimated cost of solving a structure by traditional methods. However, the efficiency of the top structural biology laboratories—even though they work on very challenging structures—is comparable to that of SG centers; moreover, traditional structural biology papers are cited significantly more often, suggesting greater current impact.

Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

* To whom correspondence should be addressed. E-mail: brenner{at}compbio.berkeley.edu

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Determination of Protein Structures--A Series of Fortunate Events.
M. Chruszcz, A. Wlodawer, and W. Minor (2008)
Biophys. J. 95, 1-9
   Abstract »    Full Text »    PDF »
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation.
T.-Y. Chien, D. T.-H. Chang, C.-Y. Chen, Y.-Z. Weng, and C.-M. Hsu (2008)
Nucleic Acids Res. 36, W291-W296
   Abstract »    Full Text »    PDF »
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction.
I. M. Overton, G. Padovani, M. A. Girolami, and G. J. Barton (2008)
Bioinformatics 24, 901-907
   Abstract »    Full Text »    PDF »
Data growth and its impact on the SCOP database: new developments.
A. Andreeva, D. Howorth, J.-M. Chandonia, S. E. Brenner, T. J. P. Hubbard, C. Chothia, and A. G. Murzin (2008)
Nucleic Acids Res. 36, D419-D425
   Abstract »    Full Text »    PDF »
Physicochemical feature-based classification of amino acid mutations.
B. Shen, J. Bai, and M. Vihinen (2008)
Protein Eng. Des. Sel. 21, 37-44
   Abstract »    Full Text »    PDF »
Robust recognition of zinc binding sites in proteins.
J. C. Ebert and R. B. Altman (2008)
Protein Sci. 17, 54-65
   Abstract »    Full Text »    PDF »
Creating protein models from electron-density maps using particle-filtering methods.
F. DiMaio, D. A. Kondrashov, E. Bitto, A. Soni, C. A. Bingman, G. N. Phillips Jr, and J. W. Shavlik (2007)
Bioinformatics 23, 2851-2858
   Abstract »    Full Text »    PDF »
PFRES: protein fold classification by using evolutionary information and predicted secondary structure.
K. Chen and L. Kurgan (2007)
Bioinformatics 23, 2843-2850
   Abstract »    Full Text »    PDF »
FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.
H. K. Saini and D. Fischer (2007)
Nucleic Acids Res. 35, W499-W502
   Abstract »    Full Text »    PDF »
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
K. Kinoshita, Y. Murakami, and H. Nakamura (2007)
Nucleic Acids Res. 35, W398-W402
   Abstract »    Full Text »    PDF »
Protein structure determination from NMR chemical shifts.
A. Cavalli, X. Salvatella, C. M. Dobson, and M. Vendruscolo (2007)
PNAS 104, 9615-9620
   Abstract »    Full Text »    PDF »
Growth of novel protein structural data.
M. Levitt (2007)
PNAS 104, 3183-3188
   Abstract »    Full Text »    PDF »
QSCOP--SCOP quantified by structural relationships.
S. J. Suhrer, M. Wiederstein, and M. J. Sippl (2007)
Bioinformatics 23, 513-514
   Abstract »    Full Text »    PDF »
Evaluation of features for catalytic residue prediction in novel folds.
E. Youn, B. Peters, P. Radivojac, and S. D. Mooney (2007)
Protein Sci. 16, 216-226
   Abstract »    Full Text »    PDF »
FireDB--a database of functionally important residues from proteins of known structure.
G. Lopez, A. Valencia, and M. Tress (2007)
Nucleic Acids Res. 35, D219-D223
   Abstract »    Full Text »    PDF »
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
L. H. Greene, T. E. Lewis, S. Addou, A. Cuff, T. Dallman, M. Dibley, O. Redfern, F. Pearl, R. Nambudiry, A. Reid, et al. (2007)
Nucleic Acids Res. 35, D291-D297
   Abstract »    Full Text »    PDF »
Rapid detection of similarity in protein structure and function through contact metric distances.
A. M. Lisewski and O. Lichtarge (2006)
Nucleic Acids Res. 34, e152
   Abstract »    Full Text »    PDF »
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry.
C. L. Dupont, S. Yang, B. Palenik, and P. E. Bourne (2006)
PNAS 103, 17822-17827
   Abstract »    Full Text »    PDF »
Comparative analysis and "expression space" coverage of the production of prokaryotic membrane proteins for structural genomics..
S. Surade, M. Klein, P. C. Stolt-Bergner, C. Muenke, A. Roy, and H. Michel (2006)
Protein Sci. 15, 2178-2189
   Abstract »    Full Text »    PDF »
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures..
E. S. C. Shih, R.-c. R. Gan, and M.-J. Hwang (2006)
Nucleic Acids Res. 34, W95-W98
   Abstract »    Full Text »    PDF »
New avenues in protein function prediction..
I. Friedberg, M. Jambon, and A. Godzik (2006)
Protein Sci. 15, 1527-1529
   Full Text »    PDF »
From genome to proteome: developing expression clone resources for the human genome..
G. Temple, P. Lamesch, S. Milstein, D. E. Hill, L. Wagner, T. Moore, and M. Vidal (2006)
Hum. Mol. Genet. 15, R31-R43
   Abstract »    Full Text »    PDF »



ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products


Science. ISSN 0036-8075 (print), 1095-9203 (online)