Related Content
Search Google Scholar for:
More Information
Related Jobs from ScienceCareers
|
|
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 laboratorieseven though they work on very challenging structuresis 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:
- Nature of the protein universe.
- M. Levitt (2009)
PNAS
106, 11079-11084
| Abstract »
| Full Text »
| PDF »
- Protein design in biological networks: from manipulating the input to modifying the output.
- A. M. Van der Sloot, C. Kiel, L. Serrano, and F. Stricher (2009)
Protein Eng. Des. Sel.
| Abstract »
| Full Text »
| PDF »
- PROCAIN: protein profile comparison with assisting information.
- Y. Wang, R. I. Sadreyev, and N. V. Grishin (2009)
Nucleic Acids Res.
37, 3522-3530
| Abstract »
| Full Text »
| PDF »
- Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.
- J. L. Ortega-Roldan, M. R. Jensen, B. Brutscher, A. I. Azuaga, M. Blackledge, and N. A. J. van Nuland (2009)
Nucleic Acids Res.
37, e70
| Abstract »
| Full Text »
| PDF »
- PiSite: a database of protein interaction sites using multiple binding states in the PDB.
- M. Higurashi, T. Ishida, and K. Kinoshita (2009)
Nucleic Acids Res.
37, D360-D364
| Abstract »
| Full Text »
| PDF »
- Solvent dramatically affects protein structure refinement.
- G. Chopra, C. M. Summa, and M. Levitt (2008)
PNAS
105, 20239-20244
| Abstract »
| Full Text »
| PDF »
- Predicting small ligand binding sites in proteins using backbone structure.
- A. J. Bordner (2008)
Bioinformatics
24, 2865-2871
| Abstract »
| Full Text »
| PDF »
- Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics.
- Y. J. Huang, D. Hang, L. J. Lu, L. Tong, M. B. Gerstein, and G. T. Montelione (2008)
Mol. Cell. Proteomics
7, 2048-2060
| 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 »
- 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 »
- 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 »
- 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 »
- 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 »
|
|